I just wanted to second Terranigma. It's a fantastic game--with great music, nice art, a fun real-time battle system--that needs more love. YouTube has some fanvids for it, if it want to check them out.
I second Gitaroo-Man. God, yes. That game rocks(!) my world. I can't play it on the Master level, but that's OK. Normal mode is fine by me.
Mischief Makers is good. I pulled this old N64 title out the other day and was pleasantly surprised. It was just as much fun as I remember it being--maybe even a bit more so! It's not a deep game by any means, but it's fun.
This one's not really unknown, but: Shadow Hearts. Specifically, the first two games. The second game, Covenant, is my favorite--the art, the story!--but you really ought to play the first game to get a feel for what's going on on Yuri's world.