Magnificent Bastard/Fan Works

Chaos from the Tamers Forever Series. Let's break it down, shall we? He has spent centuries manipulating humanity's most powerful figureheads in order to create worldwide chaos,. He is a ruthless tactician and a nigh unstoppable Badass. Not to mention being quite a hit with the ladies. (Although how much of that last part is simply his own bragging is up for debate). And he tops it all of by being witty, funny, charismatic and all in all, just a joy to watch.
Draco from Harry Potter and the Methods of Rationality took lessons on how to be one, but so far he's only a beginner. The true Magnificent Bastard of this fanfic is, of course the one and only Professor Quirrell. Without spoiling anything:
- Exhibit A: The Pioneer plaque is a horcrux.
- Exhibit B: The remains of a beautiful blue beetle are seen in his office suggesting that he has killed Rita Skeeter.
- Exhibit C: Bellatrix Black has been broken out of prison by him and Harry.
- Harry himself has the goals of a Guile Hero and the tactics of a Magnificent Bastard.
Shinji from Shinji and Warhammer 40 K, who eventually gets Gendo fired and imprisoned by punching himself in the face.

"Gendo was left alone, blinking, wondering...What the hell just happened?"

"I am Jack's smirking revenge." Directly lifted...and only adding to his brilliance.

- A few chapters later, Fuyutsuki invokes the trope by name when Gendo returns to power.
Loki, the Big Bad of My Little Avengers, who has the rather telling nickname of "The Magnificent". True, he probably gave himself the title as a bit of ego stroking, but he definitely lives up to it. At the climax of the story, he reveals that the entire plot up to that point was a Gambit Roulette: by removing Celestia as a potential threat via depowering her, he causes a Mass Empowering Event that lays the potential for the world ruled by magic he's long envisioned, and more importantly insures that Big Mac will end up with teammates -- teammates that Loki can threaten in order to force Mac to surrender Thor's powers to him. And it works perfectly, with him only being defeated afterwards due to Pinkie being a bigger Spanner in the Works than anticipated. He also shows that he anticipated Trixie's betrayal and deals with it effortlessly. Hell, he even manages to die with style -- as he lays dying from his own reflected spell, he revels in the fact that the magic released by his death will mutate all of Equestria, creating the world ruled by magic he's always wanted, then dies with a smile.
Axel is portrayed as this in almost all of Kingdom Hearts fan fic, both Canon and Alternate Universe.
The Naruto fanfic "Yakuza" makes one out of Hinata, of all people. Let me break it down for you: the Rookie 9, Team Gai, and the Sand Siblings all play a game of Yakuza, with Lee and Hinata as the yakuza. They both manipulated everyone into killing the Genin they didn't kill themselves, and at the end, Hinata betrayed Lee, causing him to kill himself in confusion, and refused to kill Naruto, leaving them the sole survivors, with Naruto taking her for ramen to celebrate. Anyone who doesn't ship Hinata with Naruto should most certainly read this.
Magnificent Bitch V in a A Cure for Love. She is literally behind everything in the first arc before she is ultimately Out-Gambitted by Light. She stole Kira's ( Higuchi's) power and she manages to fool L into thinking she is trustworthy. She integrates herself onto the Kira taskforce and L's investigation while the entire time she is in actuality the leader of Astraea, the terrorist organization that the taskforce is investigating. if not for Light and Matsuda she would have succeeded in killing L with a letter laced with sarin and if not for Misa and Rem she would have succeeded in stealing power from Kira. She is also the one who manipulated events so that Light would regain his Kira memories-this would ultimately lead to her undoing.
Alexandra de Velan of the fan-made expansion to Neverwinter Nights "The Bastard of Kosigan" definitely qualifies.
- Annoyingly, despite the fact that she and the hero are lovers, there is NO WAY to ensure she lives past the French attack on Kosigan.
Kyrio Streika, from New Dawn. While like Aizen in many ways, he prefers to masquerade as a "normal man with some interesting ideas in his head" and manipulate people and events rather than simply hit things with brute force. He absolutely never changes his bemused expression, not when a setback happens, nor when it comes time to murder someone. It is safe to say he views everyone as a chess piece...well, except for Matthew. That would be his soft spot. He is ostensibly doing all of this to help his son...though not without some genuine enjoyment thrown in.

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