Post an antagonist who turned into a protagonist.

Accelerator from To aru majutsu no index

~He first appears as a major antagonist but then became a major Protagonist after the Last order incident X3

Sort of in the 2003 anime anyhow;

Orochimaru from Naruto Shipuuden - was the good guy, then a long time the bad guy and now he's kinda helping again.

Itachi Uchiha

Vegeta from DBZ. (sort of turns into protagonist.)

Hm, I guess you can say Urara from Tsuritama.

Obito Uchiha (Naruto Shippuden)

she was evil but she became nice