I always prefer to go with intelligent races that can take class levels for villains. One of the weirdest I made was an Ulitharid (an undead mind flayer lich) with the Phantom template and a bunch of wizard levels.
But by far the toughest I made was a simple human cleric/wizard, an abjuration specialist (focused specialist from UA) with full levels in Initiate of the Sevenfold Veil. Through the use of metamagic feats, certain spells (Greater Spell Matrix, Sonorous Hum etc.) and magic items he could get off several spells in a round, and I gave him lots of nasty defensive spells like Greater Ironguard, and he had a lower-level warrior henchnman which he cast a bunch of buffs on.
On the cleric side, he had Divine Counter (use turn attempts as an immediate action to counter a spell as if using dispel magic), Battlemagic Perception, and Improved Counterspell so the party's casters had a very very difficult time of trying to get his defenses down. And he had just enough BC and Blast spells (Howling Chain, Vortex of Teeth, Great Thunderclap, Resilient Sphere) to give the party a headache.
It sounds obnoxious, and it is - he was the final battle after all. Till then I never knew how nasty an abjurer could be as an enemy.
What about you guys? What powerful/creative enemies have you conjured up?