Wow, great selection of games you've got there Tremble :)
Let me share my fav ones.
NES: Crystalis, dragon warrior 1, zelda 2 (yeah i'll be killed by this choice, but i love it xD)
SNES: Lufia 2, Lufia 1, E.V.O, Earthbound, FF6, FF5, Tales of Phantasia, Chrono Trigger, Twisted Tales of Spike Mcfang, Super Mario RPG, Secret of mana, Seiken Dentestu 3 (or secret of mana 2), Star Ocean 1, breath of fire 1 and 2, magic knight rayearth, soul blazer, illusion of gaia, terranigma (almost forgot about these!!!)
Megadrive: Phantasy Star 2, Story of Thor, Shining Force 1&2
Gameboy: Final Fantasy Adventures (yeah i know it's seiken dentestu 1 xD), dragon warrior monster 1 and 2, azure dreams
N64: Paper Mario, Quest 64
Saturn: Panzer Dragoon Saga (need i say more?... :D), Shining Force 3 (i forced myself to learn japanese to play all three acts!), Dragon Force
PSX: Brave Fencer Musashi, Xenogears, Legend of Dragoon, Parasite Eve 1 and 2, Legend of Legaia, Lunar Silver Star Story, Grandia, Granstream Saga, FF7, FF8, FF9, FFT, Castlevania SOTN, breath of fire 3, dragon warrior 5 and 7, Persona, SaGa Frontier, suikoden 1 and 3
GBA: Golden Sun 1 and 2, Mario&Luigi Superstar Saga, dokapon, FFTA, DemiKids, Shining Soul 1&2, Kingdom Hearts: Chain of Memories, boktai 1 and 2, summon night: swordcraft story 1 and 2, fire emblem: the sacred stones.
PS2: FFX, FFX-2, FFXII, Shadow Hearts, Shadow Hearts Covenant, Shin Megami Tensei Digital Devil Saga 1 and 2, Shin Megami Tensei Lucifer Call, Kingdom Hearts 1 and 2, Grandia 3, Star Ocean Till The End of Time, the whole XenoSaga, .Hack saga, Persona 3 and 4, Odin Sphere, Disgaea 1 and 2, Rogue Galaxy, Dark Cloud, Dark Chronicles, radiata stories, dragon warrior 8
Gamecube: Paper Mario Thousand Year Door, Baten Kaitos
PS3: Folklore, Eternal Sonata, Enchanted Arms, Fallout 3, Oblivion and looking forward to WKC :D
PC: This list could go on eternaly, since i love most PC RPG games, but here's a few; Baldur's Gate 1 and 2, Icewind Dale, Fallout 1 and 2, Diablo 1 and 2, Ultima 1 through 9, Elder Scrolls 1 through 3, Dungeon Keeper 1 and 2, Dungeon Siege series, Vampire: Bloodlines, Vampire: The Masquerade, KOTOR 1, KOTOR 2, Mass Effect, Planescape: Torment, Arcanum, system shock 2, deus EX 1 and 2, Avernum.
Sadly there is no DS and X360 in this list, cause i haven't got them yet :(
I'm sorry if this list got quite big, these are just my favourites...i could write books about all the RPG's i've played =D i love RPG
Edit - Oh my, i forgot about the PSP: Joanna D'arc, Crisis Core, Valhalla knights 2, Star Ocean the first departure, valkirie profile: Lenneth, Astonishia Story, Y's: The Ark of Nephilim