Let's see; from what might be considered "Classics", I'd say Huckleberry Finn. He's an independent sort who goes on a journey to help a friend, and gets perspective on how cruel the world actually is. In the end, he decides that he's had just about enough of being "Civilized" and decides to run off into Indian Territory.
From Sci-Fi I'd say Professor Bernardo de la Paz from "The Moon is a Harsh Mistress". He's kind of a subversive authority figure in the book's revolutionary movement on the moon, and is kind of a personal hero of mine.
In Fantasy books I'd say Raistlin Majere from the Dragonlance series. Kind of misanthropic and cynical to the core, yet he's a case study on what can be accomplished through sheer will and discipline, despite personal and societal adversity. Whether what is accomplished is "good" or "bad" is up to you.
In Manga/Anime I'd say Kanta Mizuno, from "Desert Punk". See the above for Raistlin Majere, except with some perversion. Still, he's an incredibly realist and strategic thinker, and I like that his pragmatism and bent towards deception in battle allows for victory over those that insist on "fighting fair".