How in the world has no one nominated
Radiant Historia - The entire soundtrack is simply amazing and the fact that they were able to fit such high-quality music onto a DS Cart astounds me.
*The Edge of Green, the game's main boss battle theme simply inspires you with a sense of urgency and compels you to beat the snot out of that stupid bear with the MT move.
*An Earnest Desire of Grey, the game's final boss theme imparts a sense of longing, loss and yet still hope. It carries you from the hopelessness of the past and into a resounding future.
Final Fantasy Mystic Quest - Really? I mean, really? Come on! Everyone loves this OST.
*Doom Castle - It wouldn't be a FFMQ nom without Doom Castle, probably one of the most memorable songs from the OST in general, if not one of the most memorable songs ever. The hard-rocking intro along with the music changing to an almost "let's climb this thing" overture really gets home what a badass place this is.
*City of Forests - As much as I want to nominate the final boss theme, I think City of Forests is a good contrast to the hard rocking style of Doom Castle. The song fills you with a sense of serenity and peacefulness that you simply won't find anywhere else in the game, especially the dungeons, which have their own very distinct musics.
EDIT: One more for good measure
Actraiser - I can't be sure what Yuzu Koshiro did before making the Actraiser soundtrack but I think this may be one of my personal favorite SNES OST's ever.
*Stage 1 - Filmore - The very second you set foot on the ground as God, you realize just what a screwed up world you're in. Trees come to life and attack you, there are dangerous bee monsters everywhere and then you're attacked by a Centaur boss! The game doesn't fool around with its stage themes and Filmore, even though it's the first one, gets you right into the action.
*Birth of the People - Meanwhile, your first foray into the town-building segment is met with a very melodious and peaceful tune to remind you of how tender and delicate you need to be as the lord of your people. It evokes a sense of serenity and peacefulness, compared to the hard-hitting stage themes.