In no particular order:

Castlevania - Circle of the Moon
Castlevania - Harmony of Dissonance
Castlevania - Aria of Sorrow
The Legend of Zelda - The Minish Cap
Megaman Zero
Megaman Zero 2
Megaman Zero 3
Megaman Zero 4
Megaman & Bass
Mario & Luigi Superstar Saga
Final Fantasy I & II: Dawn of Souls
Final Fantasy IV
Final Fantasy V
Final Fantasy VI
Final Fantasy Tactics
Metroid Fusion
Metroid Zero Mission