Top three are from DS9... "The Die Is Cast", "Sacrifice of Angels" and "What You Leave Behind" all featured some very nice battle scenes which were done remarkably well for their time.
As someone has already pointed out, though, TOS probably takes the cake for longest fights. And it's also nice to watch Kirk employ some real tactics, not just Sisko's 'evasive pattern Delta!'
Enterprise had some great ones, I was particularly fond of a lot of the 'NX-01 gets even more screwed' that was going on toward the end of the third season. And Voyager -- why has no one mentioned Voyager yet? Some of those Borg confrontations were very lively.
The Next Generation was the most actively prevent-conflict of all the shows, so while that's a great theme, it also limits the amount of things I can think of for it offhand. I'd say by extension of its very theme, the best space battles were when the Enterprise-D pulled a trump card. When two Klingon ships uncloak beside her, for example. Or when she uncloaks in "All Good Things", like the poster above me just mentioned.