I loved:
Metroid: Fusion - Great story and spin on the Metroid series, though perhaps a bit too linier, Also has a unlock for Metroid Prime (Fusion suit and origional metroid). In my opinion, best Metroid game ever, and does have some replay value in unlocking the end sequences.
Metroid: Mission Zero - Improved version of the origional, with an extra scene, AND the origional. Not quite as many endings, and I have yet to find anyone who's managed to get 100% of the items (There's one missile container that I can't figure out how to get, or can't time the charged-run-roll-ballbomb-jump-chargedflight-perfectlylinedup combo (and I have yet to find a guide explain well how to get that one))
Zelda: The Minish Cap - Lots of fun, good story, challenge was about right
Final Fantasy: Dawn of Souls - Some people think that they're not good because they (at least FF1) is easier than it was on the initial consol, but I think it was quite enjoyable.
Phantasy Star collection - It was 1-3, and 3 was enjoyable, 1 and 2 took a bit more getting used to. Could have benifited from improved graphics.
Kingdom Hearts: Chain of Memories - Seems fairly nice, though there's a few minor annoyances about things disapearing if you go into menu, and the side down 3D perspective makes it dificult to collect things at times.
Kirby: Nightmare in Dreamland - It's entertaining, a good kids game or just down time relaxing game.
Didn't like:
Earthworm Jim - No save game, so you need to play it all the way through, not good on a hand held.
Missed Opertunities:
Megaman Battle Network 3: Entertaining game, has some of the Megaman feel, and some RP feel, but advancement and improvement was a little slow on the Megaman side, so combat can become rough to play, particularly with the random card system. I've heard the others were fairly similar, some like them, some don't.
Disclamer - I am a HUGE Zelda and Metroid fan. I bought a Gameboy and later a Game Cube specificly for those games.