Prelude: The version in the FFVIII demo that came with Brave Fencer Musashi (it plays in the main menu screen that gives the game tutorial or allows you to play the demo.) It was upbeat and awesome. I am still angry it never shows up in the actual game.

Main FF Theme: The version that plays after Melodies of Life in FFIX. The two tracks meshed so well it made for a very moving experience.

Battle Theme: I don't care for many of the battle themes, in fact, I never appreciated them as musical pieces until the Black Mages did remixes of most of them. I tend to favor one time only or cinematic tracks like "Battle on the Bridge" or "Man with the Gun"

Fanfare: VI or VII's version. VI cause its the best sounding "traditional" version, VII is the best "non-traditional"

Game Over: Don't really have one...I guess VI since I can't remember any other...

Boss Battle: Decisive Battle from VI or Still More Fighting from VII. Beyond that I love special or final boss themes like "Battle on the Bridge", Dancing Mad, or the "Esper Battle Theme"

Chocobo: The Black Chocobo theme from FFIV