Hitoshi Sakimoto's Hourai Gakuen no Bouken!: Tenkousei Scramble comes to mind, I'm pretty sure nobody's ever heard of that one, haha. Some of the music sounds like him, some of it doesn't, but it's all excellent. For anyone who thinks all Sakimoto sounds the same, give this one a shot, you will be very surprised. This seriously needs an official CD release of some sort. The ending credits theme is genius!
Keeping with the theme of popular composer/not-so-popular game, how about Noriyuki Iwadare's Monstania? Lots of tracks on this sound A LOT like his Grandia stuff, especially the main battle theme. Consider this game to be Grandia 0.9 as far as the music is concerned.
Vegas Stakes is a very short but sweet musical experience. I remember playing the game as a child and tapping my feet to the music. If "Buffalo Head" doesn't get stuck in your head, I don't know what will. Fun fact: all the game's music was composed by Kimitaka Matsumae from Sega's S.S.T. Band. (It's kinda funny how I liked a game about gambling and then I grew up to severely dislike real-life gambling, hmm)
I'll throw in another vote for Lagoon, good stuff. "Atland" is one of the SNES' finest town themes. There's actually a CD release for it but the music on that disc is from the Sharp X68000 version, same tunes as the SNES one though. Naturally the SPC700 version pwns the X68000.
Don't laugh, but I've always loved the music from Mighty Morphin' Power Rangers: The Movie, composed by Hiroyuki Iwatsuki and Haruo Ohashi. I used to love the show as a kid (again don't laugh, haha) so naturally a SNES version of the "Go Go Power Rangers" song makes me very excited. But it's not just that, the stage themes kick all kinds of butt and the boss theme is speed metal to die for. It's morphin' time!
I'll try to think of some more later. That was fun. Good topic Sami.