Kyon from Suzumiya Haruhi no Yuuutsu. Simply put, I think he is a brilliant character in that show. He has a very interesting personality and his sarcastic remarks made some of my favorite moments in anime. Also, he gets a lot of character development unlike 95% of male MC's.

Honorable mentions would be Haruhi herself, Keima from The World God Only Knows, Lelouch from Code Geass and Sena from Haganai (because why not).