I like the well-known "sly snake" trope of villains. As such, they'll probably tease and communicate with the characters before they can be sure that the antagonist is indeed the villain. They know it's probable (not always though) but cannot do anything about it. Works only in a social context, however - in a dungeon there are no lawkeepers to protect those who hide their tracks well.
At the moment, I'm playing with the concept of an Anarchist mentor in Planescape. He's already been introduced to the characters as an Indep. Actually, he's the "criminal" mentor of one of the characters with the Apprentice feat. The character is a part of the Revolutionary League as well but everyone else thinks she's a Xaositect. Neither are bad people - one's CG and the other CN. It's just that they need to keep their allegiances unknown which qualifies them for this thread, in my opinion.
I'll probably sneak in an actual villain at some point. Right now the level 1 party has drawn the interest of a Quasit who knows that two out of three are fresh Clueless and the last one drew its ire by telling it to pike it. Too bad Quasit only have non-humanoid Alternative Forms. However, a Succubus ally of its or a small-time cultist of the Abyss are always possible.