Ones others have mentioned that I own (not a complete list, just ones I noticed from my own list while perusing the thread):
Enchanted Arms
The Suffering
No More Heroes
The Suffering 2: Ties that Bind
Gargoyle's Quest
Deja Vu
Demon's Crest
Ergheiz
Nightshade
Clock Tower
7th Saga
Earthbound
Blood
Suikoden (whole damn series)
Azure Dreams (one of the better stabs at a console roguelike + town sim of it's generation)
Dark Cloud 1 and 2 (the following generations even better stab at the same thing)
Steambot Chronicles
Bushido Blade (this is easily the best fighter ever, if only because it was utterly reaistic in how melee combat works, which means short brutal fights wherein your first mistake is probably your last.)
...yes, I do have a taste for obscure RPG and survival horror games, thank you very much.
Going to toss my own handful on the pile:
Shadowgate (adventure game using the same engine as DejaVu)
The Uninvited (ditto)
If the difficulty in tracking down any other than the first 2 is any indication, all 7 .hack games released in the US for PS2
Einhander (Squaresoft did a schmup)
Rule of Rose
...and the masterpiece to win the thread: Princess Tomato in the Salad Kingdom (NES).
EDIT: Forgot Rule of Rose.