I don't really have any particular final boss theme songs I like.
But I do have some boss themes in general that I find amazing.
I try to keep it a limit of 5.
FFX-Challenge. (This Song is actually played twice in the game, once fighting Seymour on Mt.Gagazet. Then when you fight Lady Yunalesca, deep inside the Zanarkand ruins.)
FFX- Seymour's battle theme. (Played during the last time you fight him.)
FFX- Summoned Beast Battle. (Played during the end of the game, when you have to fight all of your aeons.)
FFXIII-2- Giant Impact. (Played during one part of fighting Atlas.)
Resident Evil 3- Battle Against Nemesis No.1 (Played during your 1st encounter with Nemesis at the Raccoon City Police Department.)