I'm gonna list my top 2 from each game, because it's always hard to nail it down to just ONE when it comes to Nobuo F#$^ing Uematsu.
FF1: Chaos Shrine [http://www.youtube.com/watch?v=j7LR0qqsMok] (Dissidia rendition is the best), Battle theme [http://www.youtube.com/watch?v=kwNpdYPs0BU]
FF2: Pandemonium [http://www.youtube.com/watch?v=bmzXpPHw2rg] (Dissidia Rendition), Battle Theme [http://www.youtube.com/watch?v=b8TdhrqIc9c]
FF3: The Final Battle [http://www.youtube.com/watch?v=E2VbaJbJLEE], Battle Theme [http://www.youtube.com/watch?v=THsnwdDrvyo]
FF4: Four Fiends [http://www.youtube.com/watch?v=gg0fZSgs9BY] (Dissidia Rendition), Boss Music [http://www.youtube.com/watch?v=9cJe5v5lLKk] (original rendition)
FF5: Battle on the Big Bridge [http://www.youtube.com/watch?v=cxllTHj5zRI] (I know it's the FF12 version, but it makes no difference), Final Battle [http://www.youtube.com/watch?v=eQvJtPM1Ozo]
FF6: Dancing Mad [http://www.youtube.com/watch?v=JbXVNKtmWnc], Kefkas Theme [http://www.youtube.com/watch?v=qZxB4eO8X9s]
FF7: One Winged Angel [http://www.youtube.com/watch?v=PNOjhJTBQz0&feature=related] (duh), JENOVA Absolute [http://www.youtube.com/watch?v=2yX4h8Agi7U] (this one never gets much attention despite how damn good it is)
FF8: Battle Theme [http://www.youtube.com/watch?v=1orKD1ZG5KU], The Extreme [http://www.youtube.com/watch?v=RVkcmx2l3WA]
FF9: Dark Messenger [http://www.youtube.com/watch?v=v_7u16pL4As], Not Alone [http://www.youtube.com/watch?v=HFytzNhPsoM] (Not Alone is his best song, period. None of his other tracks come close to beating this song, and this version is just a work of art.)
FF10: To Zanarkand [http://www.youtube.com/watch?v=dYecLvwOiVA], OtherWorld [http://www.youtube.com/watch?v=v794Qfsn_LU]
I'd also like to give an honorable mention to Takeharu Ishimoto for his renditions of Uematsus themes. He is an excellent composer, and really does Uematsus music justice. He did Crisis Cores and Dissidias sound tracks, which really show off some of his excellent work.