I'm not sure I can choose between Clash on the Big Bridge, The Fierce Battle, and J-E-N-O-V-A. Sword of Doubt is quite high on the list too, but I don't think of it as being as much of a "battle" theme.

Also there's no "arguably" about Seymour Flux and Yunalesca being the hardest bosses in FFX (unless we're talking the International version with Penance and the Dark Aeons). They are by far the most difficult bosses in the original game.