Front Mission 4- Hostiles v Ys The Oath In Felghana - Sealed Time: Hostiles is just good for FM4. Sealed Time is good for music in general.
.hack//G.U. 2 - Gentle Hands -English- v Final Fantasy X: Someday the Dream Will End: Really classy, does an excellent job of setting the mood in-game, and reuses a main theme to good effect. Gentle Hands is good, but it's outclassed here.
Legend of Mana: The Darkness Nova v Xenogears: Flight: Sadness, both are awesome.
Soul Nomad: Cradle of the Ivory Moon v Suikoden III: Exceeding Love: Much more memorable, for all that I enjoy both.
Castlevania series- Illusionary Dance/Dance of Illusions v Valkyrie Profile - The First Unison: Easy.
Atelier Iris 2 – Resounding Heartbeat v Romancing Saga Minstrel Song - Written Invitation to Death -The Battle with Death-: Rending, slaughtering, devouring, etc. I don't think anything in AI2 could beat a RSMS boss track.
Wild ARMs 4 - Over the Wind v Chrono Cross- Dream of the Shore Bordering Another World
Perfect Cherry Blossom - Phantom Ensemble v Wild Arms XF - Blank Easel: Listening to Blank Easel again and...really not getting the hype here. It's generic WA music. And I like WA music, it's just that this doesn't try be anything but "another WA track."