All the Pokemon games work good on fGB32, in case you haven't played some of them yet...
Pokemon Crystal (which I'm starting to play now :unsure: ):
Works best at 1.66:2 resolution (full screen), FS1, synchronisation set to frame limit.
Pokemon Card Game:
isn't a big game, but it's surprisingly fun, maybe even more so than a regular Pokemon game. It works best at the same settings as above, but with the synchronisation off.
Pop Up:
A little, forgotten GB puzzle game that's really fun to play (100 maze-like levels) and has great music. You can download a remix of the music
here.
Dragon Warrior I & II:
This is ONE rom, not 2, and it is an updated version of the classic Enix RPGs for the NES. Better graphics and a more intuitive interface, and 2 GREAT turn-based RPGs.
Dragon Warrior III:
This is another great RPG, but be prepared, it's really, really LONG. It's the biggest cartridge ever released for the GBC, if that says anything. I haven't tested this on the GP32, so I'm not sure how well it works...