Most of my favorites emerged toward the end of each "generation," generally because capabilities improved. There are many other great games to consider throughout each gen, though.
1st Gen: either Stunt Cycle or Video Pinball (both dedicated Atari consoles)
2nd Gen: Mouse Trap (ColecoVision)
3rd Gen: The Legend of Zelda (NES)
4th Gen: Sonic the Hedgehog 3 (Genesis)
5th Gen: Panzer Dragoon Saga (Saturn)
6th Gen: God of War 2 (PS2)
7th Gen: Xenoblade Chronicles (Wii)
8th Gen: ?? (time will tell... expecting new greatness
)