[112B2018]

Mother 3 only has limited tracks and there's no complete version

Star fox assault has a promo with 9 tracks but no official soundtrack

There's quite a few examples of arranged soundtracks without an original soundtrack like the original F-Zero for example.
Edit: Most of F-Zero SFC can be found in "Nintendo Super famicom Game Music" (TOCT-6429)

There is no version of Assault suits Valken with the SFC music.

Every Animal forest/crossing album only contains the "K.K." tracks

Ganbare Goemon~Neo Momoyama-(aka Mystical Ninja Goemon 64) tracks do not loop

Super Donkey kong and Super Donkey kong 2 have sound balancing issues, and all versions of DKC2 are missing the track "mining melancholy"

I almost bought a copy of Metroid sound in action last year, I'm glad I didn't, for what it's worth the NSFGM album I mentioned earlier and Play it loud Vol.1 have some tracks from Super Metroid looped and in decent quality.

Thanks to everyone on this forum for bringing attention to these, same with Mother 2 and Mystic Ark and the others mentioned here.
I was considering buying the GBA Castlevania soundtracks, Star ocean, and Tales of Phantasia too.
I'm still waiting for a CD release of Plok...

Edit: I found another one, the Elebits soundtrack is missing some of the best tracks, both of the tracks I consider the best in the game are not included...