Can't really decide. The DS version of 'This is the Last Battle' (as FF III's Final Boss track is called, at least in the oirginal OST) is very great, if not one of my favorites.
The original version of 'This is the Last Battle' is a great track as well, but I think not many people have heard it. A real shame, for its a great track (and the first Final Boss music in the series), especially when one considers that its on the NES.

I love 'The Last Battle' from FF IX as well.

The Extreme, The Final Battle (FF X's Final Battle) and Dancing mad are excellent choices are great runner ups...

Nah, I'll go with "This is the Last Battle (DS)". Simply because the entire battle with CoD in FF III DS screamed "EPIC!!!" at me.

'The Last Battle' is my second choice and all the others come after it.