The crews have evolved on worlds with orientation, so their psychology and conventions reflect the reality that they are planetary creatures.

Orson Scott Card captured the importance of orientation to human psychology very well with his "The enemy's gate is down" line in Ender's Game. Changing the perception of orientation changed the psychology of the strategies in use. Instead of working from a perception of inferiority due to being outnumbered, they worked from a perception of positional superiority to offset their weaknesses, even though the facts of the battle had not changed.

Even though "orientation" may have limited practical applications in space, the psychology of living beings demands an orientation for the purposes of communication and conceptualization. Even in unlimited space, beings that evolved on planets will tend to gravitate (no pun intended) to formations inspired by two dimensional thinking.

In our world

When you watch a movie, the ships are usually aligned. This is because of reasons that are most likely not based on our experience in space battle. I'm pretty sure I read about this and I will update if I find the reference. Here are some reasons:

• Visual aspect. A viewer is expecting that an organised fleet of spaceships will look, well, organised. If all the ships were facing another direction, some up, some down and everything in-between, then it would look like a random mess. Nearly as if the fleet had suffered a problem and were not battle-ready.
  
  


• In movies, armies of barbarians wear random colours and are not well aligned. A proper army is wearing uniforms, move as one man and is well aligned.
  
  


• The humanity likes to see aligned things. The movie spectators as well.


• Experience in sea battle. What might be intuitively closest in our experience to a space battle is a sea battle. Sea battle very often were lines of ships passing along each others and shooting. The bigger battleships were even called "Ship of the line".
  
  


• Classical view of battles. Before the first WW, the typical way of fighting was to align people in front of each other and make them shoot or advance toward the enemy to engage. (Or at least it is what we think about it.)
  
  

All these points might have influenced our idea of what a battle should look like, and is hence what we get in movies and other fiction works about space battles.

In your world

On the other hand, your question might also be in-universe, which means applying the logic and the rules available within a story.

So, if the ships of your world are well aligned, it might be because of one of these reasons:

• It's the early age of space battle, so generals don't really know what to do and try to hide it by spending energy on aligning the ships. To them, a well aligned fleet is the sign of a good general.


• Weapons and shielding are mainly at the front in order to save weight. So you want the front of your ships to face the enemy. If both fleet are applying the same logic, you get two well aligned fleet. (Until the her comes and decide to attack the enemy from behind and then the strategy changes).


• Similarly, propulsion is at the back, so if you want your fleet to be able to accelerate in one specific direction, they need to be aligned.


• Coordination. If someone shouts "Watch out, missile coming from above!", then you want everybody to look in the same direction. Same with the order "Ship XXI, move forward"!.


• Because of all the points in the first part of my answer, a well aligned fleet could impress the enemy more and ruin its morale.


• They are all coming from the same point. For instance if all the ships were attached to a structure facing one direction and they all moved along the same path to get to the fighting scene, then they maybe simply had no reason to turn.

Are you asking from the POV of TV shows and Movies?

TV shows and movies always show fleets approaching one another in the same orientation and on the same plane. Why? For the convenience of the viewer and to better express the drama of the moment. The chaos of a true 3-D fight is very difficult to follow on a 2-D screen. An example might be the opening battle sequence from Star Wars, Revenge of the Sith, where a 3-D battle is briefly shown with a quick transition to focused views of Skywalker and Kenobi flying their fighters. Just enough to let the audience understand the chaos, then shift the point of view for easier viewing (allowing the movie to focus on dialog). Note that even that battle wasn't as chaotic as it could be. I'll mention that in a moment.

My point is, while humans see in 3-D, only experienced military fighter pilots have a grasp of 3-D combat — and even that's affected by the fact that they're flying over a gravity well. I'm thinking of a quote from Mr. Spock from The Wrath of Khan, "he's intelligent, but inexperienced. His patterns indicate two-dimensional thinking...."

The real thing: gravity wells

In reality there would be a lot of navigational complexities affecting the nature of 3-D fleet combat. The most obvious is a gravity well. Unless your world uses gravity-nullifying technology (crews always experience "down" with the correct amount of force), the natural habit of pilots would be to orient the ships for the greatest opportunity for the crew — which means orienting the ship so that the floor is between your feet and the planet. The closer you are to a gravity well, the greater the tendency to do this.

Where you see 3-D combat taking place in this situation is very much like terrestrial fighter planes: altitude. Your orientation may tend to align with the gravity well, but your combat is taking place at different altitudes.

The real thing: Open Space

Let's go to the other extreme: deep space. Not a gravity well worth mentioning in sight. In this case, your combat has more to do with approach vectors and the design of your ship than anything else. This would be the most chaotic (from a 3-D perspective) combat. Ships flying upside down in all sorts of directions, etc. Anything goes. Kinda...

You see, most of our fantasy ships are designed from a 2-D perspective. The ship has a keel, somewhat like an ocean-going vessel, guns are mounted along that keel or axis. There's a "front" and a "back" and the engines are at the "back." They're long, flat, and there's a distinct "down" to the design that's almost always represented by the "bottom" of the ship. Even the design of the spherical Death Star from Star Wars was a series of laterally-oriented floors or decks from the "bottom" of the sphere to the "top."

What this means is that your combat will conform to how you can bring your weapons to bear. If you're flying a Star Wars "Star Destroyer" or the U.S.S. Enterprise, your orientation can't really be universal without serious mobility of the turrets/launchers. You can get around this to some degree by using, for example, heat seeking missiles, which remove orientation as a factor of launch, but your beam weapons are limited by placement.

Therefore, to really enjoy the orientless nature of deep space battle, you want a spherical ship with concentric decks where "down" is the geometric center of the sphere. Weapons are mounted uniformly on the surface of the sphere. The sphere can enter battle from any direction, move in any direction, rotate in any direction, and perform its tasks equally well.

The real thing: rocks

Space is big. Really big.^{Citation Needed} as a consequence, outside of gravity wells you're actually unlikely to encounter anything. Asteroid belts aren't the densely-packed fields of boulders we see in the movies (if they were, gravity would pull them together to form planets). Planetary rings are nothing at all like what was shown (delightfully, I might add) in (if I remember correctly) Star Trek (2009) when the Enterprise comes out of warp in what looks like an opaque soup of gas, to rise out and save the day. It looked cool. Rings are nothing like that.

That doesn't mean there aren't rocks to be avoided. Terrestrial fighter pilots are moving so fast they are forced to care about where mountain tops are. Mountain tops don't occur very often — but when they do it's, um, inconvenient. Rocks are the same thing. You'd be on constant look-out for the little bounders because your deflectors are probably designed to move dust aside, not rocks, and certainly not boulders or things the size of a mountain.

Why do these rare events matter? Because they create a plane upon which combat takes place. That rock, (because we grew up running and playing in a gravity well) will quite easily be interpreted by our minds as "down." Something we want to be "away from." It would be believable (but not required) for combat to begin forming along 2-D lines should a big old rock be found in space.

Which leads us to my last entry....

The real thing: debris

I suspect space combat will result in a lot of debris^{Citation Needed} that doesn't conveniently fall to the ground.^{Citation Needed} That debris is theoretically chaotic: expanding in all kinds of directions. Because of this, you'd think that it would force combat to an even more chaotic, orientless, 3-D condition.

Well... maybe...

Combat isn't as chaotic as one might think. Strategies are being put into play. Organized and intentional maneuvers are used. This means the debris field is developing and being manipulated in complex but theoretically predictable patterns. As the debris field grows and our natural childhood-driven tendency to see it as "down" or something to "stay away" from takes hold, it is (in my mind) quite believable that combat begins to develop on 2-D planes (-ish. That would be an awfully simple way to model a very complex situation, but I think you get my drift here). The "plane of debris" or "surface of the debris cloud" would force the battle, giving it a "down."

Conclusion

But, to conclude, I personally think ship design and our personal perception of gravity has the greatest affect on whether or not space combat has an orientation or alignment. Engines will be seen as "back." The first time we're given a database on any particular ship, its design will be presented and we will assume the top of the screen represents "up" and we'll pretty much always think of it that way forever more. Mostly because we grew up on a planet where there was a distinct "down" and "up." You might not have noticed yet, but how we're trained to perceive our universe as children is actually a very hard habit to break — which is one reason why just any terrestrial pilot cannot be a successful fighter pilot.

But, in your world, if you design your ships to take advantage of 3-D, you'll find that training will follow and the tendency to impose order on chaos will dissipate. With the exception, as I said, of gravity wells. If you don't have a way to remove them from the picture, the planet below will always be "down." Childhood — a very hard habit to break.

Because front and back.

Making the assumption that the fleet operates on what is (Star Trek) called impulse power, such propulsion typically (as far as "typical" applies to imaginary subjects) has a fixed thrust vector relative to the ship orientation. In plain language, you point the nose in the direction you want to go, and something comes out the back to make you go there.

If the fleet is going to maneuver as a fleet, everybody has to point in the same direction. So that takes care of one axis.

As to other axes, there is no apparent reason to think that all of the ships will orient themselves the same way. For instance, it would make a great deal of sense to concentrate all energy point defense weapons on one side of the ship, then keep that side pointed toward the enemy. So a fleet would proceed with the strong side (let's call it the top) pointed away from the center of the formation. To do otherwise is to reduce the effective firepower caused by other ships masking their lines of fire and/or fratricide.

Of course, in movies and such it looks cooler and more like the naval formations we're all familiar with if everbody has the same orientation, and the Rule of Cool is the real, underlying cause for an awful lot of what you see in the movies.

There are some practical reasons for organizing a fleet in a space battle:

1) You don't want your T crossed. This is what happens when many enemy ships can range on your lead ship but only your lead ship can range on the enemy ships. If you fail to meet the enemy fleet basically as a plane your T gets crossed at least for a while. The more combat involves beam weapons the more important this becomes. (Note that if you have any non-combatant ships along they will be behind this plane.)

Note that movies tend to get this wrong--your fleet should be in a 2D plane, not a 1D line, and they should be arrayed in a hexagonal formation, not a square one.

2) Assuming your firepower is any fashion directional (and basically any beam weapon must be directional) you will in general be able to deliver a harder punch if you build your ship with a this-side-towards-enemy design. Likewise, you will put your best defenses on that same side.

3) When the stuff starts flying you will want to maintain communications links with at least nearby ships despite enemy attempts to interfere. (If your sensors are blinded you can engage the inbound with info from your neighbor. If your missile director is out he can guide your missiles.) This will be most secure and reliable if you have dishes pointed at your neighbors. You get maximum flexibility if the fleet starts out with those dishes at the middle of their travel. This means you will be aligned to one of the standard angles for which your fleet is designed to operate.

If the mounting space for weapons is a factor then you'll end up with basically cone or pyramid shaped ships, the point towards the enemy. (This assumes there's nothing about your tech that forces some other shape. For example, in the Honor Harrington universe the drive forces ships to be long and narrow.)

Which of those angles is only relevant if humans actually relay data as part of the communications. If someone is going to say "fighters coming in high" then everyone needs to have the same definition of what up is. If all such communications are "fighters!" and a data packet showing where they are it won't matter which angle you are at.

Because they are fighting in orbit. There's actually little reason to fight in deep space. There's nothing there to fight over and if you tried to intercept an oncoming fleet on its way to your planet or asteroid you'd end up whooshing right past it with a split second interval to exchange fire. But planets provide an automatic thing to orient yourselves to and you're going to want to put the smoother side of your ship if it has one toward the planet to reduce drag if you end up skimming the upper atmosphere.

Most spaceships in "space opera" science fiction movies are badly designed.

Written science fiction is more likely to use better designed starships than movies and television, but includes many that use the wrong layout.

In most visual science fiction starships use some type of generated gravity aboard for convenience in filming scenes with normal weight instead of weightlessness. It is also common in written science fiction but not nearly as much, because writers don't have to worry about the extra expense and difficulty of depicting weightless conditions aboard ship.

If a space ship uses gravity generators to generate gravity aboard ship, the designers have considerable freedom, depending on the technical aspects of that highly advanced fictional technology, to arranged the decks of their ship.

In most space opera movies and TV shows the decks are arranged parallel to each other so that some are "above" or "below" other decks. Thus one part of the ship's hull is more or less the "top" according to the internal gravity and the opposite side of the hull is more or less the "bottom" according to the internal gravity.

And that seems like a reasonable way to arrange the internal gravity and decks of a starship if it is technically possible to generate gravity that works like that. So far so good.

But where most space opera movies and TV shows, and many written space operas, goof up is arranging the their space ships like sea ships, with the decks running in the direction that the ship travels, and thus the direction of the generated gravity being perpendicular to the direction of travel.

Suppose that the space has to suddenly accelerate and decelerate by several times the amount of the generated gravity, which should be kept at 1 g for the sake of the health of human characters. Characters will be flung forward or backwards with a force of several gs. I remember a story where a character killed another character by turning on the propulsion while the other character was not strapped in a seat. And they were both in the relatively small control room.

Imagine walking down a long corridor facing fore and aft when suddenly, without warning, the spaceship accelerates or decelerates at several gs. You will suddenly find yourself in a vertical elevator shaft and fall to your death.

Items not tied down but instead held in place by the generated gravity will suddenly fly around and smash into other objects and people.

The Black Hole (1979) had a large space ship the Cygnus with a very long corridor. The Cygnus also had rocket engines at the rear. Whenever the rocket engines fired the very long horizontal corridor would become a very tall vertical shaft and anyone in it would fall to their deaths.

If a spaceship with that design accelerates or decelerates at several gs, the ship could compensate for that by increasing the force of the generated gravity it uses. But that generated gravity would be working at right angles to the g force from acceleration or deceleration and thus would turn the total g force acting on people and objects in the ship into a diagonal vector somewhere between pure horizontal and pure vertical.

But if a fictional starship is designed not like a sea ship but like a skyscraper building, being tall and thin with many decks one above the other, and with the front and the top of the ship being the same part, and the back and the bottom being the same part, it would make much more sense.

The decks would be perpendicular to the direction of travel, and so the generated gravity would point toward the back/bottom of the ship and away from the front/top of the ship. The generated gravity would work in the same direction that the ship traveled. So if the ship accelerated or decelerated the strength of the generated gravity could be increased, decreased, or reversed, as needed to compensate for the changing g forces and keep the total force acting on the passengers a steady one g pointed downwards.

So a starship with generated gravity built like a skyscraper would probably be shaped like a very tall cylinder. The decks would probably be circular and relatively small, with many levels of decks.

So a fleet of space battleships would probably be a bunch of tall, thin cylinders, and probably be arranged in some sort of three dimensional pattern with all the ships in the fleet pointed parallel, with their fronts/tops pointed in the direction the fleet was traveling in.

Since the best type of battle is one where you can harm the enemy but they can't harm you, weapons range will be very important in space battles. If it turns out that Fleet A can damage the ships in Fleet B at a distance of up to 1,000,000 kilos but Fleet B can only damage the ships in Fleet A at a distance of 100,000 kilos or less, Fleet B will try to keep the distance between fleets at 100,000 kilos or less, and will head toward Fleet A to lessen the range if necessary, while Fleet A will try to keep the distance between fleets between 100,000 and 1,000,000 kilos and will move toward or away from Fleet B if necessary to in the proper range.

Presumably the total sizes of the two fleets in a space battle would be a small fraction of the distance between the two fleets, so that all the ships in a feet were firing at the enemy at basically the same distance, just as in the early 20th century battleship battles were fought at longer and longer ranges by fleets widely separated from the enemy fleets.

And the hypothetical thin cylindrical starships would keep their fronts or backs pointed at the enemy fleet in order to have as small a cross section as possible pointed at the enemy weapons to make as small and hard to hit targets as possible.

Most movie and Television space opera starships use the in my opinion inferior design based on sea ships, with the decks orientated in the direction of travel and thus with the generated gravity perpendicular to the direction of travel. Thus those in my opinion goofy starships have tops and bottoms which are not the same as their fronts and backs, but instead are perpendicular to their fronts and their backs.

So when those goofy starships fly forward they have four sides perpendicular to their fronts and backs, a right side, and left side, a top side, and a bottom side.

And it seems like there is no reason for two such spaceships traveling together to be oriented with their top and bottom sides pointed in the same directions. Two spaceships travelling side by side could have their topsides pointed toward each other, and their bottom sides pointed away from each other, or vice versa, and it wouldn't matter as long as they were far enough apart for their generated gravity to not interfere.

And if a starship coming from star system A happens to meet a starship coming from star system B in interstellar space, there is absolutely no reason to expect that their top to bottom axis would be aligned parallel instead of pointing in tow different random directions.

If the two starships are travelling under power when they meet, their two fronts should be facing forward and thus toward each other. but if they are coasting through space with their engines shut off there wouldn't be any reason for either ship to keep its front pointing in the direction of travel.

I could probably imagine some sort of technobabble explanation for why typical space opera starships based on the designs of sea ships might all have their generated gravity pulling the in the same direction, but I am not fond enough of those goofy starship designs to suggest any sort of justification for them.

Movies are not the best source for realistic space ship and space warship design.

The principle of a space warship are its tight mass limits and the long range at which combat happen, which means your enemy is usually attacking from a single direction, and you want as little armor as possible, forcing you to a long and narrow cylinder, as the sloped armor gives you significant gains. Since your engine is usually not armorable, you want to put it at the opposite side of your armor pyramid, facing away from the enemy.
Lasers, particle beams and guns will generally face forward. Missiles can point anywhere, as they can reorient after launch.

The orientation for the crew is independent of the orientation of the warship. It could without an orientation, using all four walls equally.
A long distance warship will likely start including spin gravity, in which case the internal orientation of the crew is 'down is outwards' since that is where the spin gravity will be pulling objects.

Actually, orientation is very important even in space because coordinated movement is difficult to achieve without a common frame of reference.

To give a simple example: To avoid midair head-on collisions, airplane pilots are instructed to change their heading to the right to avoid collision. Such a rule makes perfect logical sense under normal circumstances, but suppose that one of the planes was upside down, and they both still decided to turn right: In that case, they would crash. It follows that having a common orientation would be critical anytime when a human pilot would be expected to follow standardized flight rules, even in space.