That's a tough one. And I don't think it's fair. From one generation to the next, music in video games has evolved quite a bit.
And each console had its own quirks for the music chip. Some later consoles played directly from CDs.
On the NES, I think Megaman 2 and Journey to Silius had kick-ass chip tune soundtracks.
On the SNES, I'd say Uniracer had a great rock soundtrack. Star Fox also had an epic soundtrack. Oh and Killer Instinct was fantastic. It even came with a music CD with the soundtrack. But my all time fave has to be the TMNT IV game soundtrack. And I'll give a special shoutout to Chrono Trigger.
On the Sega Genesis, I think the Sonic series had an amazing newjack and fusion jazz style soundtrack.
On N64, and PlayStation I particularly LOVED the Wipeout racing game soundtracks with music from my all time favorite electronica bands of the time. Goldeneye 007 holds a special place in my heart as well.
After that it gets really hard because so many games have incredible music. It's hard to choose.