Favorite: Gundam Federation vs. Zeon. Capcom Gundam fighting game goodness, plus it's one of the few fighting games you don't need to be super skilled at fighting games to master.
Hated: Dragon Ball Z Ultimate Battle 22. JANK. Horrible fighting game that looks like dog doo doo and plays just as bad. The saturn port, from what I gather, is better than the psx.
I remember that one Yugioh TBS game (Capsule Coliseum pretty sure) which I used to love as a kid even if I couldn't understand the mechanics and just winged it. Aside from that... can't think of anything else, except the inverted case (games that were later given anime adaptations).