Uchiha Madara, Pein, Uchiha Itachi, Hoshigaki Kisame, Konan, Deidara, Hidan, Sasori of the Red Sand, Hyuga Neji, Hatake Kakashi, Jiraiya, Nara Shikamaru, Gaara of the Desert, Hyuga Hinata... well that should be enough of a list.
Note: They are not in order since really I don't have a #1.
Those are some of my favorite characters in Naruto though. To continue would take forever since the number of characters I like far outnumbers those I dislike.