3e:
Beholder: Saw this suggestion on a forum. A giant floating bag of faces. Each "face" moans, screams, or curses the individual. Each vocal effect is an eye beam.
Bugbear: Low-tech
Yautja-type of hunters.
Choker: Creature with snakes for fingers, reptilian features and translucent scales (story: A cult who were trying to get closer to dragons were using an artifact that was mutating themselves horribly. The subject above used to be a halfling).
Dire Ape: A beast made of half-decomposed plants and roots, hungry for flesh. The only stat change was to take the adhesive ability from a mimic, so that weapons were caught in the mushy, root-filled flesh.
Elemental-Water: Blood Elemental, on two different occasions. Each incarnation healed when it did damage, but the first one had a dual "Shield Other" and "Half-heal the caster" going.
Ochre Jelly: Vomit Monster. (Story: Fiendish infestation of a lost colony. The characters vomit gallons of black fluid, and then the stuff stands up and attcks. Tough fight that unnerved the players.) It could function just as easily as a Ward.
Owlbear: With a poisonous bite, it works as a fantastic psionicsless yaun-ti abomination.
4e:
Displacer Beast: A shadow cultist (not mine).
Ettercap: Adding a Shadowborn Stalker template, it became a creature that stole its victims shadows, allowing it to control its victims at night.
Hyena: War dogs.
Guard Drake: Hell hounds.
Orc Raider: Blade Devil; a spined devil's little brother, with blades jutting up all over the flesh.