Werewolf is a themed game of Mafia, played with a supernatural enemy (werewolves) instead of organized crime. The role names are different to those in mafia: there are Villagers instead of Townies, Seers instead of Cops, etc. but otherwise the games are identical.
As the person who came up with the idea of "Werewolf", let me note that I intended it to be the same game as Mafia, rule-wise. I only changed the role names. I guess that makes it a Theme Game in the sense used on this wiki, but in the "fictional theme" sense, not the game-mechanics sense.
Since then, I've heard people refer to "Werewolf" and "Mafia" as related games with slightly different rule mechanics. I didn't hear what they thought the difference was, though. -- Andrew Plotkin