Hmmm, I can't remember all the ones I should list here, but here's some that I liked enough to remember and post here:
"Restart Shootout" - Hidan no Aria
http://www.youtube.com/watch?v=DrEHa8guyiI
"Blue Tiger" - Code Geass R2
http://www.youtube.com/watch?v=QfmuNcOWxYI
"Elephant's Scream" - Needless
http://www.youtube.com/watch?v=3So2gboFzYQ
"B13a" - Bleach: Fade to Black - Kimi no Na wo Yobu(not sure if this song ever got a proper title
):
http://www.youtube.com/watch?v=TJzxpmOogqg
"What's Justice" - Code Geass R2
http://www.youtube.com/watch?v=ArjtnKFUVnM
"Lieu de la bataille décisive" - Shakugan no Shana II
http://www.youtube.com/watch?v=VM1wvoK-nMQ
"Hoshi no Kagayaki" - Magical Girl Lyrical Nanoha The MOVIE 1st:
http://www.youtube.com/watch?v=nN5o6PV_AQc
Battle against Walpurgis Night, "Surgam Identidem" - Puella Magi Madoka Magica
http://www.youtube.com/watch?v=5Ak4bt7qJ6k
"Last Battle" - Katanagatari, a piece truly fit for the finale of the series, probably my second favorite battle theme period.
http://www.youtube.com/watch?v=buf4IvOQkjE
My top one was easy choice, Grimmjow's battle Theme from Bleach "Power To Strive"
http://www.youtube.com/watch?v=eOGkZsuFILU