Man, that's a tough choice.....
"Coin Song" from FFVI comes to mind as a favorite, I think just because of the scene it evokes between the two brothers flipping a coin to determine who has the misfortune of taking the throne. That little scene is some of the best writing in the series, or any series. It's pretty much the same melody as the Figaro castle theme, which immediately anchors it in your mind about what and where and who the track is about, but shifts the tone to give it an entirely different meaning soaked in a feeling of nostalgia, memories, almost happy, almost sad.
I feel like I have to name one other, and that's "Into the Darkness" from FFIV. It was the first RPG I really properly played (other than some dabbling with Dragon Warrior II and III as a kid, which mostly consisted of running in circles outside town and killing slimes until I ran out of HP and died and started over). That track in my mind is the definitive dungeon theme, as it just evokes such a feeling of vast, dark, mysterious places. I can't walk into a cave or spooky dark place in real life without hearing that theme in my head.
As you can tell, the scene a track evokes tends to be a big thing for me. One of my regrets in life is that I am not in any way musically trained, so I can't talk about the composition or harmony or sinewaves or whatever musical jargon to explain what makes a track good to me. For me, it's all about a mental image of a place or a scene that a track builds. This applies not just to game soundtracks, but to all music I enjoy. I think this is probably a direct result of all my earliest favorite music in life having come from video games, where music does indeed tend to be associated with and define specific places as you move around the game.
OK, OK, one more thought to throw out there. When playing FFVIII, the soundtrack didn't really stick out to me like the soundtracks of previous games had done. But when it came to the piano collections later, the FFVIII piano collection actually does stand out as my favorite. I think it just shows that there's a lot of potential in these tracks where if one version doesn't jump out at you, a remixed/alternate version can give it some new life and create an unexpected favorite.