More detail would be nice. Are you looking for an entire mini campaign arc? A single fight? A plot hook? What ECL? What books? What party?
That said, here are some generally flexible BBEG ideas for a few.
Earth
Spirit
Water - ambitious four-armed Sahuagin Fleshwarper, manufacturing an army of four-armed Sahuagin.
Death - a Lich is inventing new variants of Skeletons and Zombies, and has already depopulated several towns for more raw bodies.
Domination - aristocratic Vampire Rogue attempting to dominate/sire the king and become the power behind the throne.
Evil - Cult of the Blessed Agonies attempting to bring a demon lord into this world
Cold - a charismatic leader has the entire north worshiping a 50-HD Gargantuan Polar Bear (normal intelligence and behavior) as a symbol of the inherent superiority of the north
Fire
Alien - Tsochari invasion. Nuff said.
Knowledge - Gnomish Artificer worshiping Boccob is on the verge of inventing a nuclear bomb, and plans to test it soon.
Glory
Air
Mechanics - the rules governing when Inevitables are dispatched become corrupted somehow, and suddenly they start hunting people down for every minor offense.
Forest - the Wild Hunt rides the land. Nuff said.