There are three Fort Joy decisions, one Arx decision, and one decision on the Lady Vengeance that reward the Villain tag; otherwise, you can get the Villain tag only by murdering a total of three innocents with or without Source Vampirism.
Decisions (MASSIVE SPOILERS)
- Fort Joy: Trick Unnis into giving you all her gold
- Fort Joy: Side with Griff's thugs during the shakedown
- Fort Joy: Kill the Dreamer and report back to Griff
- Lady Vengeance: Subjugate the Figurehead
- Arx: Destroy Arx with the Doomsday Device
There are no other ways to get the Villain tag. Anything else that has been suggested is just coincidence (e.g., killing spectators in the Fort Joy arena) or not a contributing factor (e.g., leaving everyone on the prisoner transport ship.)