My pick:
- Pokemon -
Pokemon R/B/Y
Pokemon G/S/C
If hacks also count, then Pokemon Prism
Pokemon TGC
- Mario -
Super Mario Land
SML 2 - The best platformer ever, in my humble opinion
SML 3 - Wario Land
Wario Land II - Best Wario platformer ever, in my humble opinion
- Other (haha) -
Tales of Phantasia Narikiri Dungeon (practically unheard of I think, a half sequel to ToP. Translation patch is out there somewhere)
Final Fantasy Adventure (First in the Mana series)
Final Fantasy Legends I II III
...That's about it, really.
EDIT: Oh yes, Zelda: Links Awakening DX, Oracle of Seasons and Oracle of Ages.