Capcom Versus SNK 2, definitly. I didn't like Cap VS SNK 2 EO all that much, though. The Cube's controler just isn't made to handle traditional 2D fighters. *Sigh* I was somewhat disappointed. The SNES was so great in the department of handling any type of game, but neither the N64 or the Cube can do that very well.
Of course, you could argue that 3D games weren't really all that common back then, but that's irrelevent. The PSX(2), while I'm not saying it's better or worse, is quite able to handle any type of game thrown out there. For the most part, that is. The PS2 handled Cap VS SNK 2 very well. I just hope, Nintendo's next system will be the one to live up to the SNES' legacy. So far, the N64 didn't make it, whether you want to argue it's due to lack of 3rd party support, and the Cube hasn't really shown much of anything besides a handful of quality games and a bit of potential. We'll see, I guess.
I digress, overall, I like Cap VS SNK 2 the best. My favorite series of fighters would be the Street Fighter games. How could I not love them, growing up with them. Mortal Kombat was alright, but it wasn't near SF, in my opinion. I've also enjoyed SNK's side of the ring as well. King of the Fighters were pretty good too. (Mmm, Mai...) But, yes, I think after reading all of this, you know my answer to this topic.