nes- festers quest and blaster master (sunsoft new how to make games back then, both games are AAA most will never play), also duck tales was great

arcade- rastan

snes- mickey mouse adventure game (? name),

neo geo- magician lord, recently slammed by screw attack, I say screw u screw attack, this game was amazingly good for it's time, also nam 75 kicks ass

genesis- nothing but overrate crap on that system, maybe herzog zweii

saturn- astal (beautiful hand drawn goodness no on ever played)

ps2- fatal frame, r-type final, maximo

game cube- dk jungle beat, what else can be said about a game best played with you shirt off, loved it, also luigi's manson, paper mario, and wario world- those were all great

Secret of Evermore, Crystalis and Little Nemo are excellent choices.
The Battle of Olympus and NBA Hangtime are my choices. Few have played Battle of Olympus, but it's one of the best games on NES, which is saying something. Plus it's about a thousand times better than Zelda II. As for NBA Hangtime, it's simply the best game ever made...and Gamespot gave it 4.x on N64!

the guardian legend

Civ Rev for the 360

arcade- rastan

SMRPG Legend of the Seven Stars. It released at a completely wrong time in the transition from 2D to 3D games in the N64/PS1 era and was therefore overlooked.

Killer 7 (PS2/GC), Viewtiful Joe (GC/PS2), PNO3 (GC), JazzJackRabit (PC), Okami (PS2/Wii), WarioWare Touched (DS), Beyond Good and Evil (GC/PS2/XBOX), Panzer Dragoon (DC), MGS: The Twin Snakes (GC).

Disgaea 3

Its a great, great game, almost  endless gameplay, tons of humour, tons of classes, attacks, objects, missions, etc...

Its simply great. Its fun as hell. But, what? are those 2D charcters? Is that an SRPG? Oh, then its crap.... ¬¬

MGS: The Twin Snakes (GC). you're right this game was a blast but no one bought it

Alien Front Online. And yeah, the Fire Emblem series is a good choice.