i would have to say Itachi, he did take out the majority of the edo's, and stopped kabuto.
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so a enemy commander and the every single member of a immortal army except one, that has to give him rep.
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for me the top three would be
1. Itachi
2. Naruto(he did stop the majority of the zetsu's and some of the edo kages, and saved alot of fodder)
3. Orichimaru(brought back the 4 kages, saving the allaince from certain destruction, and in the process did turn sasuke into a good guy, something not even naruto could do)