Xenogears
It's an amazing PS1 RPG with one of the best storylines of any game, my favorite RPG battle system of all time, 3 dimensional characters, and very appealing graphics. The game would be even better if it weren't for the obvious budget and time constraints that crippled it. It truly is a wonderful game, and a remake of it with Xenosaga III graphics would quite possibly make my heart explode.
Heh, I agree on that. Xenogears was an amazing game with a great story and colorful characters. The battle system was innovative and fresh. Graphicly it wouldn't at all match the standards today (it's worse than Mario 64 damnit), but it still adds a lot to the game. Not my favourite, but a great one.
My favourite game would have to be Diddy Kong Racing, Banjo-Kazooie, Donkey Kong 64 or Link's Awakening. I can't really decide as all games are absoultely wonderful, and some of Rare's masterpieces for the N64 are just stunning. The creativity and effort put in those games (even though BK and DK are Mario 64 gimmicks) are astounding. All the characters are loveable, and DK and BK set the standards after Mario 64 for adventure-puzzle games.
Diddy Kong Racing was one of the first racing and N64 games I played, and it really left a mark. Racing in the beautiful scenarios, with fun missions and great replay value I really hold it has one of my favourites.
And then Link's Awakening. My first Zelda-game, which deserves more attention than it currently gets. Sure, it's a quite mainstream Zelda-game, but the trading sequences, the photo man and the humour throughout the game really adds to it.