Other than the already-really-beloved boss battle themes (Force Your Way, Dancing Mad, Battle With Magus, etc.), one I've always found underrated is Lufia II's link to DS version's battle 2 remix
. Kinda standard hard-rock-guitar stuff going on, but I really like the licks and how bright the trumpet sounds. Even in the SNES version.
And of course they aren't RPGs, but shout-outs to Divine Combat (The Binding of Isaac) and Fast Track to Browntown (Super Meat Boy). Love Danny Baranowsky.