Nier vs LoM - I need to play Nier, for the music if nothing else. May have to borrow from someone at DLC. But...LoM music is so hard to beat.
Final Fantasy 6 vs Castlevania Symphony of The Night - SotN stuff is good, yeah...but...I dunno. The music always felt like background music, rarely standout. Where ff6 has several songs I will never forget and did thier job amazingly in game.
Muramasa vs Chrono Cross - the saving Marbule scene is what tips this. I love that song, and the use of it in game there was great. Sliiiightly peeved at CC for my favorite song from it(Dragon God) only coming up like...what, once? But eh, so it goes.
Ar Tonelico II vs Final Fantasy 13 - Hmm...yeah, see SotN for FF13 here. The music is clearly good, but isn't standout. Note I've still only played half the game, but AT2 music is good enough that I'm willing to vote this way anyway.
Final Fantasy 3 vs Megaman 4
Dragon Warrior 4 vs River City Ransom