Separate tracks are too numerous so I'll just post playlists of soundtracks considered by me to be among the best ever.
Cave Story (PC, 2004), Pixel. Most amazing chiptunes I've heard in a while.
Gradius V (PS2, 2004), Hitoshi Sakimoto. Excellent "orchestral music meets intelligent techno" takes on Konami's glorious tunes.
Deus Ex (PC, 2000), Alex Brandon. The whole soundtrack is tracker music, btw. The same guy wrote the score for Jazz Jackrabbit games.
Battle Garegga (Arcade, 1996), Manabu Namiki. Widely considered to be his best soundtrack, especially since the rest of his work is mainly remixes on himself and other people.
Earthworm Jim Special Edition (Sega CD, 1995), Tommy Tallarico. It's
that better than the already good original score.
Darius Gaiden (Arcade, 1994), Hisayoshi Ogura.
Donkey Kong Country 1 & 2 (SNES, 1994 & 1995), David Wise et al.. Perhaps the best example of quality SNES music (at least one that doesn't come from an RPG).
Alien Soldier (Genesis, 1995), Norio Hanzawa. Likewise, the best Genesis soundtrack as I see it, and probably my favorite from Treasure aside from Gradius V and Ikaruga. Couldn't find a playlist on YT.
Jets'n'Guns (PC, 2004), Machinae Supremacy. I find it their best album as well, some tracks are among my favorite metal renditions of chiptunes.
Guess that's all for now.