Duck Tales - The Moon
Mega Man - Cut Man
Mega Man 2 - Dr. Wily Stage 2, Wood Man, Air Man, Flash Man, Password Screen, Title Theme
Mega Man 3 - Snake Man, Spark Man, Gemini Man
Mega Man 4 - Dust Man, Bright Man, Skull Man
Mega Man 7 - Shade Man, Freeze Man
Bubble Bobble - Isn't there just one song? xD
A link to the past - Pretty much anything
Ocarina of Time - Forest temple, Gerudo Valley, Twinrova
Majora's Mask - Stone temple, Deku Palace, Clock Tower
Street Fighter 2 - Ken's Stage, Guile's Stage, Vega's stage
Sonic - Emerald hill zone, Green Hill zone, Marble zone
Chrono Trigger - Wind Scene, Frog's theme
Mario - Mario bros 2 ending theme, Dire Dire Docks and give it 10 more years and I'll add Good Egg Galaxy to this list as well.
Mystical Ninja: everything
Lost Vikings: everything

Some single picks:
Tomb Raider Theme
Lost Vikings 2 dark ages
Battle Arena Toshinden, Eiji's Stage.
That one song in EVO search for Eden.
Dr. Mario: Fever
Act Raiser: Fillmore

Not going to bother with Final Fantasy music. I'd be here all night.