Now that I have the topic rolling ...
For the campaign I am winding up, I have had several villians. I suppose the real big bad guy was the Slumbering God. A God of Madness and Chaos entombed in a demiplane tied to the land the PC's are in. One of the big goals for them was to free the Slumbering God without allowing him to roam freely through the Prime Material Plane. (It is a campaign thing. Trust me, it would have been bad if the God had done that.)
Of course, I suppose that is more a goal than a villian. But, the god did have a small cult of worshippers that had a home base right outside his barrow. Sounds like they would be the bad guys right? Not quite. Ages ago, a Nalfeshnee (and his babau cohort) was banished to the Prime Material Plane. The Nalfeshnee has been stringing the cult along to guide their power while he was implementing his schemes for world domination (Muhahahah). To do this, he teamed up with a pair of lichs. One Cleric, one Wizard, putting together an army of undead.
The PC's haven't really encountered any of these until late in the game. So far, they interrupted the ritual the Nalfeshnee was directing and left before any fatalities were incurred. For the record, the party achieved their goal - interrupting the ritual. Fighting the Nalfeshnee to the death was not required. Experience wise, I will give them ~40% exp since they knocked the Babau down to 1 hp before he was able to teleport away and they frustrated the Nalfeshnee to no end. I will also tack on a hefty goal bonus for interrupting the ritual. Especially since they bagged on the Nalfeshnee so they could teleport home to help defend against the undead army assaulting their home town. Remember the Lichs?

They have wiped one of the lichs and I am not sure if how they will do against the other.
So, those were some of the big movers and shakers. But, they did have a recurring villian at lower levels. She was the abducted sister of one of the PC's. Brought up, through the machinations of the Nalfeshnee, to hunt down and kill the followers of her father's God. It just so happens that two of the PC's follow the same god. She is a little whacked in the head (Remember the Slumbering god of Madness? Permanent Magical insanity and she is MPD.) She was a Ftr5/Sor9 when the party managed to save her. Once they saved her, restored her mind and swayed her to the path of Good, she was able to tell them a lot about the Nalfeshnee.
Let's see, so far in my game, I count a Demon, undead Cleric, undead Wizard and a combat sorceror for my villians.
I also have a monastary of LE monks being led by an Erinyes with Cleric levels.
Looking at everything, I have a lot of magic using villians. For some reason, I never really contemplate the standard fighter or rogue. Admittedly, this game has been decidedly non-urban, so the lack of a rogue might stem from that.
For my next campaign, I am looking at a much more urban backdrop so politics can really come into play. I would love to have villians that the PC's know they could wipe the floor with, but they can't touch them due to political influence. While I like making nice combat creatures, they certainly the end-all-be-all of villians. So, I like to hear what other people have done.
