Sci-Fi:
Laton from Peter F. Hamilton's
Night's Dawn books. Completely amoral, ruthless and possessed of a brilliance degrading the best minds of humanity to mere dilettantes. He's the most wanted 'criminal' after driving a thinking, feeling habitat and close to a million immortal thought-constructs insane with a genetical engineered virus before destroying it and its population of several millions
as a diversion for his escape. Firmly on the way to immortality and distributed existence within a network of controlled minds, he's possessed by a spirit returning from death (in a scifi setting, no less) and analyzes the threat to humanity posed by the dead, finds a solution, 'vampirizes' the possessing spirit and blows up a few million possessed souls before departing into the afterlife, telling the rest of humanity that there is a solution, but that they have to discover it for themselves. He's only a 'supporting character' appearing for only short time, but he outshines many of the main characters.
Aenea from Dan Simmon's
Endymion books. It's not easy being the messiah 'destined' to liberate humanity from the oppressive control of the Core, the multitude of parasitic AIs, that have perverted the church and almost the whole of human society into unwitting processing units, all the while knowing, that she will die a painful death at the hands of the church. But Aenea manages. (Note that I'm only discussing the book, not RL religion)
Incidentally the two represent my favourite Science-Fiction books.
Fantasy:
Ben Adaephon Delat, aka Quick Ben from Steven Erikson's
Malazan Book of the Fallen books. He's only a mortal wizard in a world, where gods and other beings of terrible power play their games on the back of mortals, but he still beats them at their own game. Planning, outwitting and using unfair advantages are what he excels at, and damn is he cool. Quote: "Who are you?" "In the eyes of the gods? Only a mere sandworm ..." (at which point he uses a rare species of worms to unravel necromantic bindings, he couldn't even touch in matters of raw power).
In no specific order:
Anomander Rake, Icarium & Mappo Runt and Whiskeyjack (MBotF), FitzChivalric Farseer & Chade, Vlad Taltos, Munuel (Höhlenwelt).
There are a few others, but my tired mind can't produce the names. It's no coincidence, that MBotF features so prominently, as I'm currently in the process of reading it yet again.
