Yep. The never ending debate. Which Sci-Fi universe would beat another.
To give everything a level playing feild, I am going to say remove super fantastic powers, so universe changing force use from SW is out. Basically, cap it at Palpatines lightning. I think what the most critical part of an inter-universe conflict would be the application of space fleets. This is where sci-fi wars would be won/lost. Simple matter really: if the ships die in space, the fight can't be fought on the ground.
Size Comparisons here. Click on -10x for best grouping.To me, it would come down to Star Wars and 40k here. Star Trek is just too small and weak. Borg Cubes are impressive, but Star Trek ships can beat them and I bet Star Wars and 40k woop star trek. Phasers are sooooo small and short ranged in comparison to the fighting of 40k and star wars. All the other ones suffer the same fate really. Alien, Battlestar Galactica and Starship Troopers are way to small. Halo is to far behind in technology but is at least approaching Star Wars size ships. I don't know enough about babylon 5 and macross to really compare, but just on size basis I am going to remove them.
I personally think here that 40k wins. They may not have the biggest ships, but the Empire only had 8 super star destroyers. Meanwhile, the Imperium possess thousands, if not tens of thousands, of their battleships. And then there are star forts such as a Ramilles class or even bigger things like Port Maw. Those are HUGE! and allow several battleships and cruisers to dock with them.
And you can see the GUNS. Point out where the turbolasers are on that super star destroyer. Can you. I know approximately where some are, but I can't see them. Meanwhile I can point out all the major weapon systems on the 40k star ships. They launch 30m torpedos instead of measly 1m proton torpedos. Bigger guns = bigger boom.
Next is the escorts. A 40k cobra escort is 800m long (the link I provided is wrong, but firestorms and swords are 1.5 km long so imagine that on the link provided). The smallest military vessel is 800 m. A star destroyer is twice as long yes, but it is suppossed to be the center of an Imperial fleet in Star Wars, but 40k has ESCORTS just as big.
And next is range of battle. I am taking the visual cues from Star Wars and imagining that the battle takes place at those relatively clos ranged, 10-20 km apart. That is like a WWI naval battle really.
40k happens thousands of KM apart. They only see the ships on sensors for the most part and it is rare that they are in visual range, and when they are, it is pure destruction. One ship will not survive and the other will be crippled.
Then there is ship protection. In Star Wars sheilds are falling like every minute it seems, and those ships are not armoured heavily. The true protection of a 40k ship is in its armour. Sure the sheilds help, and in the fluff fall kinda often too, but 40k ships are plated in meters of armour.
The one advantage Star Wars possesses I believe is fighter technology. Their personal star ships seem better than 40k ones, especially since they are sheilded (for the most part). But to me it is not enough to take on 40k capital ships, which possess as much if not more point defence than a Star Wars ship.
Oh yeah, and Necrons and Nids I think could chew up any other universe.
So tell me what you think. Poll over there -->
*FACTIONS RULED OUT- UNIVERSE ON UNIVERSE
Will talk about ground fighting some other time
POLL RESULTS
Who would win in a space battle?
Warhammer 40k 25 (65%)
Star Wars 3 (7%)
Babylon 5 5 (13%)
Star Trek 3 (7%)
Macross 0 (0%)
Halo 0 (0%)
Other (Post in comments) 2 (5%)