Two of my personal favorites would have to be the soundtracks for
Dragon Quest Monsters (GBC Black Cart), and Gameboy Camera. With DQM I felt like all of Sugiyama's music really lent itself well to the channels available on the GBC, with the quality of the sound being filled out really nicely. I say that game in particular, because I guess I have a better memory of it than DQ 1+2, though i'm sure the music from that cartridge is just as good.
Starlit Night is my overall favorite from that game. The 3DS remaster of that track didn't even come close to capturing the flying feeling the original track had. It's also super clever in how it works within the limitation of the GB sound chip.
Gameboy Camera was incredible because it's just a great expression of Tanaka's more experimental sounds (for the tracks that were his). Funny enough though, my favorite track from that was probably the most orthodox track in the game, the
Credits music (after the fanfare. I absolutely love the melody, and the way the bass voice moves in the B section makes me all warm inside). Though the
Title Screen music is super cool too! While it sounds impenetrable at first, it's ridiculously complex for a GB track, the way it samples the main
Mario 1-1 theme and the little call and response stuff in it is super cool and expertly constructed.
This one is good too, with simple loops that are catchy and have a really distinct aural identity. Some of the sounds Tanaka got out of the GB chip is totally nuts. There's plenty more good in there too, but it's an underrated gem that makes good use of short-form loop-based composition and has a large variety of small tracks.