Still far too many for a full list, but here are a few that I own that I'd really like to get around to playing one of these days:
Crystalis (NES)
Willow (NES)
Secret of Mana (SNES)
Earthbound (SNES)
Final Fantasy II (SNES)
Final Fantasy VII (PS1)
Paper Mario (N64)
Record of Lodoss War (Dreamcast)
Skies of Arcadia (Dreamcast) or Skies of Arcadia Legends (Gamecube)
Kingdom Hearts (PS2)
Star Wars: Knights of the Old Republic (Xbox)
I'd also like to play through Chrono Trigger again.