Here's my list, movies only...
1: Enterprise E vs Scimitar. Hands down the best for me, I know it has it's detractors but it's everything a Star Trek space battle should be - the sight of the E unloading everything it had at the Scimitar was awesome, the movement of the ships, new type of Romulan Warbird (would have still preferred a D'eridex mind), topped off with the ramming sequence was the highlight of an otherwise derided movie.
2: 1st Reliant attack in TWOK. This one just shades number 3, I just love the build up, the tension, the music, the noise the phasers make - one of TWOK's many brilliant scenes.
3: Mutara Nebula battle in TWOK. As near as makes no difference as good as number 2 for similar reasons...
4: Fleet Battle in FC. Great for the sheer scale of it and amount of ships involved. Dating fast though.
5: Opener from ST09. Just an all round great sequence, brilliant FX, camera tipping all over and proper phasers!
6: Khitomer battle TUC. Entertaining battle, I like the FX when the cloaked BoP fires, and some great camera angles as it attacks from all over the place. Great seeing the Excelsior in action. Not as visceral as I wanted it to be though.
7: Vengeance warp attack. Strange one, this as it's not technically a battle as the Enterprise didn't fight back. Top notch FX as you'd expect from a year old film, the noise the Vengeance makes as it bears down on the Enterprise is absolutely incredible and makes the scene as good as it is. It's waaaay too short though, and would have made it into the top 3 if the Enterprise had got the chance to fire back a few times - a missed opportunity to make a classic Trek scene for me.