Hmm...off the top of my head:
Last Battle (Self Determination) - Breath of Fire III; Akari Kaida and Yoshino Aoki. It's basically the same song as the final dungeon, but modified to fit the characteristics of the battle. It's also quite impressive.
Decisive Battle! Saruin! - Romancing SaGa: Minstrel Song; Tsuyoshi Sekito, Kenji Ito. It's a remake of the original version of the song, which was done between Nobuo Uematsu and Kenji Ito (if my memory serves me right), which was remastered while adding Sekito's guitar riffs. It's quite impressive, since it's basically the second song of a two-parter battle, essentially when things get serious.
Dragon God - Chrono Cross; Yasunori Mitsuda. Let's face it; if you've played the game, the real final boss is a joke. The actual final boss really should have been the Dragon God, since it's much more challenging to face. It also boasts having an awesome song to boot.
Howl of the Departed - Lost Odyssey; Nobuo Uematsu. Also the CGI title loop theme song, but it's heard correctly in the final battle. Essentially, it's a rock opera with Ominous Japanese Chanting broken quite roughly by...wait for it...a guy rapping in Japanese. The sound of the clock out of rhythm is quite impressive.
Last Battle - Coon - SaGa Frontier; Kenji Ito. Really, all of the final boss theme songs in SaGa are amazing (of special note, the girls get good theme songs), but this one is special. It's...kind of melancholic, but then it blasts into action right in the middle, sort of like a wave. If you play the game right before that point, you'll probably notice how it seems to fit mentally with the situation. Bonus points if, during the crescendo, you unleash a 5-person combo.
Nachtgall/MiBgestalt/Todesengel - SaGa Frontier II; Masashi Hamauzu. Now, you must be wondering...I'm not a fan of Hamauzu, and I consider him mediocre at best, but if there is something to listen, is the set-up for the final boss of SFII. First you start with a lullaby, then with the theme song of the game (and the battle theme, and so on), then you finish with an entirely different and rather upbeat song. It's one of the few compositions I can actually like from him, and I still stand his best work thus far is SaGa Frontier II (though I personally prefer Ito over Hamauzu). Please play them in order; I can't stress this enough.
The Sacrifice, part III - Seiken Densetsu III; Hiroki Kikuta. The first part of The Sacrifice is depressing, evocating the feeling of despair from the final boss. The Sacrifice part II is still depressing, but more like struggling rather than anything else. Then the song stops, the final boss gets his second wind, and you get this song...which is pretty darn impressive, since it's actually inspiring and uplifting. Knowing that once you fight this battle, the game is over is doubly inspiring. Really, really, really inspiring.
Falling Down - Mega Man Zero 4; Ippo Yamada, Luna Umegaki, Tsutomu Kurihara, Masaki Suzuki, and Akari Groves. This one I must admit is from a game I haven't played, and someone else allowed me to hear. What you hear is a song using the GBA sound hardware (or an emulation of it), which makes it all the more impressive considering what they do with it. They have a remastered version which...starts great but then it kinda sucks compared to the original.
Bookmarks