Luffy vs Crocodile
Luffy vs Lucci CP9
Ichigo vs Byakuya
Kenshin vs Saitou
Kenshin vs Soujiro
Gintoki vs Jiraia
Gintoki vs Jirocho*
Naruto vs Sasuke

This post was edited by TsukiBaka on Aug 16 2012 05:05am

Naruto vs Pain ofc

shirou vs archer
shirou vs gilgamesh
pretty much all the fights in katanagatari
alicia vs selvaria

This post was edited by douglas22888 on Aug 16 2012 07:41am

Kagura and Shinpachi vs. Abuto (wouldn't say best but pretty awesome)
Gon vs Hisoka (2011 version) http://www.youtube.com/watch?v=znEu-FxJ7Xw
Kurapika vs. Ubogin (can't wait for the remake of this arc)
Alphonse vs Pride and Kimblee (dub warning)

A lot of fights from FMAB are really good
Gintoki vs Hosen
Hijikata vs Isaburo (One of my favorites)
Luffy vs Crocodile
Luffy vs Lucci
Sword of the Stranger (like someone else said all the fights) (final fight http://www.youtube.com/watch?v=xryoNrqhyI )

There are a lot more I am probably missing

This post was edited by LyZeR on Aug 16 2012 08:23am

Shikamaru vs Hidan

Goku vs Frieza
Gohan vs Perfect Cell
Piccolo vs Android 17
Goku vs Kid Buu
Naruto vs Pain
Pain vs Jiriaiya
Kakashi vs Zabuza
Spike vs Vicious
Ichigo vs Aizen
Kenpachi vs Nnoittra
Ichigo vs Grimmjow
Ichigo vs Byakuya
Ichigo vs Ulquiorra

Yeah I don't watch much anime.

Kenshin vs Sourjiro #1 to me, maybe vs Saito too, depends.

ichigo vs all

luffy vs croc
naruto vs pain
aang vs fire lord ( not sure that this counts as anime fights but still epic)