Well, let's start from the bottom (and i'm assuming you've already played, or at least tried, most of Nintendo's own games. Although there were a lot of good ones on the GameCube). (These lists are in no particular order)
GameCube: Skies of Arcadia, Tales of Symphonia, Doshin the Giant, Prince of Persia: The Sands of Time, Beyond Good and Evil, Ikaruga, Chibi-Robo.
PS2: Persona 3 FES, Persona 4, any Shin Megami Tensei game, Shadow Hearts (all 3), Disgaea (1 & 2), Atelier Iris, ICO, Shadow of the Colossus, Klonoa, Jak and Daxter, Ratchet and Clank, Dragon Quest VIII, Okami, Psychonauts, Onimusha, Valkyrie Profile 2: Silmeria, Odin Sphere, Sakura Wars: So Long, My Love, Tales of the Abyss.
DS: Okamiden, The World Ends With You, Rune Factory (any), Ace Attorney (all), Ghost Trick: Phantom Detective, Avalon Code, Might & Magic: Clash of Heroes, Dragon Quest (any in main series), Final Fantasy III and IV, Luminous Arc 1 & 2, Soul Bubbles, Radiant Historia, Shin Megami Tensei: Devil Survivor, Shin Megami Tensei: Strange Journey, Chrono Trigger, Advance Wars, Bangai-O Spirits, Rhythm Heaven, Lunar Knights, "Nine Hours, Nine Persons, Nine Doors", Etrian Odyssey, Super Scribblenauts, Golden Sun: Dark Dawn, Hotel Dusk.
PS3: I don't own a PS3, so i'm not sure how qualified i am to comment on this. However the following is a list of games i've heard good things of, and plan to buy when i get a PS3 later this year: Demon Souls, Disgaea 3, Valkyria Chronicles, BlazBlue: Continuum Shift, Eternal Sonata, 3D Dot Game Heroes.
I'm sure there must be something in there that interests you that you haven't played.