Some ideas:
A Gorgon would make perfect sense. It's roamed the ancient city for such a long time that its petrifying breath has long ago turned every living thing to stone. Maybe advance it a bit. Only problem I could see with this, is that a gorgon isn't very subtle, and can be easily dealt with using force.
A pack of Phase Spiders living within the ruins is led by a particularly nasty and cunning one (perhaps a half-fiend, a half-elemental (MotP), or a corrupted (BoVD)). The Phase Spiders lurk on the Ethereal Plane and attack one at a time, biting a creature, hopefully poisoning it, and then retreating. If the players find their lair and kill the Nasty Phase Spider, the pack disperses. Otherwise they have to deal with the constant threat of ambush from an unknown number of spiders.
An old Druid who worships the earth has long ago made the old ruin his home. He lairs there with a group of Phantom Fungi 'pets' that slowly wander the ruins, looking for food. He also has a shambling mound that he keeps near him at all times. He is reclusive, but not evil, however he is very crass and uncivilized. He may be bargained with, but he takes a dim view of anyone who harms his precious 'pets.'
Long ago, the city partially merged with a pocket of the Plane of Shadow and a small pack of Shadow Mastiffs call the place their home. Their 'pack leader' is a particularly vicious Bugbear infused with the taint of the place (basically, he has the Shadow Template found in either
Lords of Madness or
Manual of the Planes), who has made a home out of one of the old buildings where the taint of shadow is the strongest. Perhaps the secret of the city's ruin lies within that building, and the bugbear doesn't even realise it.
The kaorti (outsiders from the Far Realm,
Fiend Folio) have begun to establish a Kaorti Cyst within the middle of the city. Trapped here when a fluctuating portal to the Far Realm collapsed, the Kaorti plan on finding another way back home... or perhaps plan on bringing more of their kind to the Material Plane for some nefarious purpose. Perhaps the elves accidentally opened the portal to the Far Realm long ago and that caused the ruin of the city. If so, the architecture of the city may have been subtly warped over time, ie trees have become petrified or turned into ropy masses of flesh that seep ichor. Buildings may randomly groan and twist, stone may have become spongy and sport alien orifices (a building covered in eyes that open when the characters venture too close, or maybe a giant sphincter doorway
).
A colony of feral mongrelfolk (
Fiend Folio) and a group of Myconids (
Monster Manual II) call the old city their home. The two groups frequently battle each other in the streets and they see the arrival of the PC's as a way to 'further' their cause. When the PC's first arrive, they are shadowed by unseen forces (Mongrelfolk or Myconids) and are finally approached by both parties who offer them a deal: Help them fight their enemies and the myconids/mongrelfolk will help the PC's however they can. Though neither the myconids nor the mongrelfolk are evil, they still battle each other over the remnants of the city. Why they do this, they don't know. What they do know is that they have done this as long as they can remember. What NEITHER of them know is that they were once the elves who lived within the city, transformed by a magical experiment gone awry (is their any other magical experiment?). Whatever the cause of the experiment, it ruined the city and warped the elves. The PC's need to decide which side to ally with (if any) and maybe uncover the secrets of both race's pasts.
![:]](http://www.enworld.org/forum/images/smilies/devious.png "Devious :]")
