Let's give this a whirl... I'm avoiding ports and remakes to make this more fair.

NES: Mega Man 2
Genesis: Sonic and Knuckles
Game Boy: Pokemon Red/Blue
SNES: Chrono Trigger
Playstation: Xenogears
Gameboy Advance: Final Fantasy Tactics Advance - If I allowed ports, it would be Final Fantasy VI Advanced
Playstation 2: Metal Gear Solid 3 and Shin Megami Tensei Persona 3 - I seriously can't decide between them.
NDS - The World Ends With You
PSP - Kingdom Hearts: Birth By Sleep
Playstation 3 - Assassin's Creed Revelations
Wii - Xenoblade Chronicles/Legend of Zelda Twilight Princess
PC - Civilization 2

I have a few other systems I could try to list but my experience with them is not large enough to make a fair judgement. I also forgot how crappy the Game Gear was because I can't fathom a title for the life of me that was actually good on that thing...