I am pretty nerdy about such things so I could list them all day, but I'll try and think of a few most of you probably haven't encountered (plus the good CC and PSX era FF songs have been exhausted already anyway - though I'd definitely encourage those who haven't to check out some of the remixes for The Man with the Machine Gun).
FF has been beat to death so I'll try to veer from it a bit, but for a game few people were able to play FF11 had some really nice tracks... I remember the first time LordS and I got to a few areas we just kind of stopped and listened, which isn't something that tends to happen in MMOs.
Some ambiance themes:
http://www.youtube.com/watch?v=ZtCs2LWOV1c (Selbina)
http://www.youtube.com/watch?v=clld-gFL050&feature=related (Ronfaure)
There's a ton of really great songs on that soundtrack though, it's a shame it didn't get more listens.
Battle themes always tend to be well received, so here's a few more of those
http://www.youtube.com/watch?v=Wk9fbj4q-i0 (Time to Raise the Cross, Tales of the Abyss)
http://www.youtube.com/watch?v=R1uJb6itOG8 (odd pick, but Heavyarms' Stage from Gundam Wing: Endless Duel)
http://www.youtube.com/watch?v=jDlzk1WE9V0&feature=related (Arabian Dream, Kingdom Hearts)
http://www.youtube.com/watch?v=6WdibZ37hdw (Bastard Sword, Breath of Fire 4)
http://www.youtube.com/watch?v=2A4tHe7wR2U&feature=related (Aska' Stage, TMNT: Tournament Fighters)
http://www.youtube.com/watch?v=uGOUrmIe0ck&feature=related (Battle With the Demons, Lost Odyssey)
And one that isn't really battle theme paced, but since it was a series with underappreciated music in addition to gameplay I felt like I should give it a nod
http://www.youtube.com/watch?v=XIyue_ddvkM&feature=related (IMA vs. FIMBA Cup Battle, Monster Rancher 2)
Some other random tracks:
http://www.youtube.com/watch?v=2tSaWMrRlx4 (Ethan's Theme, Heavy Rain)
http://www.youtube.com/watch?v=MOJ91H4mraU (The Price Of Freedom, FF7: Crisis Core)
http://www.youtube.com/watch?v=qoGuIL4H3Cs&feature=related (A Man, Breath of Fire 4)
http://www.youtube.com/watch?v=jXAs...82E5AF292&playnext=1&playnext_from=PL&index=1 (The Champion, Breath of Fire 3)
http://www.youtube.com/watch?v=35L-8s_N-aY (City under Siege, FF9 - maybe the most effective music track of all time as far as getting me in the mood)
http://www.youtube.com/watch?v=C2yd1AU2jyo (Miror B's theme from XD yeah !!! (which is technically a battle theme but whatever))
http://www.youtube.com/watch?v=cdvRpbCCyzw (Redemption, Heavy Rain)
http://www.youtube.com/watch?v=JQ1u1m_3KbM (Fable 2 theme, which I love just for the music box at the beginning)
http://www.youtube.com/watch?v=3uhk5iCM8V0 (Painful Memories, Heavy Rain)
(Seriously, just listen to the whole Heavy Rain soundtrack - it's the only thing I ever have or ever will buy on iTunes. It wasn't on YouTube when I wanted it, but I like paying for things of this quality, anyway.)