I don't think I've played a game that I enjoyed more than Paper Mario for the Nintendo 64. The bosses are fun,
the music is fantastic, and the replay value is immense. I think I've gone from start to finish around fifteen times.
As for runners up, I'm a big fan of the Legend of Zelda for the NES (probably my next favorite game), Zelda: ALttP, TTYD, Super Mario RPG: LotSS, Mario & Luigi: Superstar Saga, and the NES Super Mario games (including Lost Levels for the Famicom/VC). I also love the
Donkey Kong Country and Castlevania series (especially, DKC2, Castlevania III, and Super Castlevania IV). I've been hearing great things about Symphony of the Night, but alas, I do not have a PS.
I bought these games on VC and plan on playing them for for the rest of the summer:
Chrono Trigger (
awesome game; finished, beat most sidequests afaik -- I don't look at walkthroughs, so I'm not totally sure),
Metroid (finished;
loved this one, except health farming was tedious),
Super Metroid (finished with 67% item completion; I should aim for 100% the next time I run through the game), Ys Book I and II, Mega Man 2, Mega Man 3, Mega Man 9, Mega Man X, Final Fantasy VI, and Contra III: The Alien Wars.
I may also play through the second quest of Zelda (NES), and Castlevania I and III if I get the chance.