Presented not in order of preference, but in (roughly) chronological order. I think it's interesting to hear how much the music evolves with each video game console generation (each generation noted in this post with a different color border).
Bubbleman - Mega Man 2
The Moon - DuckTales
Cossack Stage 1-2 - Mega Man 4
Opening - Sim City
Life in the Mines - Donkey Kong Country
Dire, Dire Docks - Super Mario 64
Requiem for the Gods - Castlevania: Symphony of the Night
Dream of the Shore Near Another World - Chrono Cross
Gusty Garden Galaxy - Super Mario Galaxy
Red Carpet - World of Goo
Still Alive - Portal