Chrono Cross- People Seized with Life/Prisoners of Fate v Disgaea 2 - Elegy of the Tundra: Elegy sounds nice, but...People Seized with Life is just freaking awesome.
Xenosaga 1 - U-TIC System v Wild Arms ACF - Murdering Princess: If nothing else, Murdering Princess wins this based on "I remember it in game!" Xenosaga 1 music tends to lose points a lot for, you know, really horrible usage in game to the point where you say "wait, I don't remember that song..."
Final Fantasy 4: Battle with the Four Fiends v Phantasy Star II - Death Place: Worst part, Death Place is about as good as PS2 music gets. Four Fiends isn't bad, but there's definitely better in FF4, so...yeah...
Suikoden V: Rhapsody in Battle/Dancing Rhapsody v Final Fantasy X - Otherworld: Pretty clear cut to me. Otherworld is unique yet good, the Suiko 5 song is...pretty generic and takes a while to really get anywhere, and when it does, its nothing special.
Baten Kaitos - Survival from the Force v Metal Saga - Driving to New Fork: Both are decent, but liked the former more.
Fire Emblem 7 ~ Together, We Ride v Final Fantasy Tactics - Lucavi Battle theme: ...another song from FFT I think is one of the weaker ones? Geez, what the hell? FFT has some good songs, but why are people nomming shit like this instead of the awesome stuff like Antipyretic (IN FAIRNESS! Lucavi Battle works in game, but its horrible alone.)
Flipside, Together We Ride is bad ass.
Atelier Iris 1 - Deceitful Wings v Secret of Evermore: Greek Temple: Nice Final Boss theme vs. Song I actually said "wait, this was in SoE?" when I listened to it, still can't tell you where it plays despite playing the game 3 times, and its really nothing special when it comes down to it.
Tales of Symphonia - Rest of the Heart v Phantasy Star Online Episode III – “Idola the Strange Fruits”: Whatever, this song stuck out to me more, which is sad since I had played ToS and still couldn't recognize the song.