Can't name a single favourite, but off the top of my head:
-Aang vs. Ozai
-Zuko vs. Azula (more for the themes/visuals than the actual combat)
-Korra vs. Vaatu/Unalaq (not the giant battle, only the polar/gateway one)
-Spider-Man vs. Venom (Spectacular Spider-Man series, both battles)
-Sonic vs. Metal Sonic (Sonic OVA)
-Twilight vs. Tirek (deal with it! XD)
I'm going to include the Freiza battle in 'Dragonball Z' because while like most DBZ fights it has the padding issue, However, I recently read some pieces as to how and why DBZ (and Dragonball as a whole) should have ended with the saga, from both a thematic and narrative standpoint. So if I were to take it as the case, and the series ended there as per the supposed original intent, then yes, I'd count the battle as among my favorites. While other fights might have been done better supposedly (haven't seen that much of the series admittedly), I feel that beyond Freiza, things started getting rediculous, what with constant character resurrection and multiple super saiyans...gah), which adds to a whole lot of gripes I have with the series as a whole.