Write them as a real person, with real motivations driving their actions and thoughts. Their actions might resemble a villain's. Don't downplay or water down their evil traits or flaws though — a feature occurring in Draco in Leather Pants.
Making them physically unattractive helps — Beauty Equals Goodness is a big part of Draco in Leather Pants — but if you go to Gonk levels, there's still a chance of them being re-imagined as a sympathetic grotesque, or as Ugly Cute. Plus there's a chance of people utterly ignoring appearance in their Self-Fanservice, as Magus can attest — he Looks Like Orlock in official art, but Fan Art makes him a White-Haired Pretty Boy.
Putting them across the Moral Event Horizon will cost them their Anti-Villain status, but have them swerve near it on a bad day. Have them injure a child for their "cause" — even if they treat it as being Necessarily Evil, their karma will take a ding — or have shades of Politically Incorrect Villain.
edited 6th Mar '11 10:35:29 AM by KillerClowns
How do I write the Anti-Villain without running into the Draco in Leather Pants factor?
edited 6th Mar '11 9:48:37 AM by TheProffesor