One Piece:

Chopper/Usopp vs. Mr. 4 and Miss Merrychristmas: A bit long, but had some funny parts, some "dramatic" parts, and ended great too.
Luffy vs. Crocodile (final one): Like Shik said, very satisfying. :] Memorable music, too.
Chopper vs. Gedatsu: Chopper's time to shine! (About time, too)
Sanji/Zoro vs. Groggy Monsters: Probably doesn't count as a "battle", but this was a fun one!
Luffy vs. Foxy: Quite amusing, and the ending was cool.


FMA:

Ed vs. Roy Mustang: Very interesting fight- the beginning of it was especially hilarious, and the battle itself was great.
Ed vs. Greed: Short, like they all are (unfortunately :[), but was fun enough to watch- especially since Ed finally had a chance to actually win this time.

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My OOT Parody Thread. "Chapter 68: The Shadow Temple, Part IV- It's Hard to Get a Tan When There's No Sun Anyways" has been posted 4/13/08.
[Best Parody Fic S07/W08]