Birch Spirit: these are the souls of murdered dryads, which now live in birch trees and spectrally reach into a humanoid's heart to kill it.
Blood Spirit: The 2E supplement Shaman had an interesting take on spirits, which were not undead but rather creatures of belief and emotion. The blood spirit was a CN spirit that existed to stop the suffering caused by bullies and tyrants on the part of the oppressed. These spirits possessed bullies and got them to stop their tormenting by either getting them to kill their victims or let them go. Blood spirits are also fond of contacting those who help the underdogs and could grant lilmited protection spells to shamans. Probably would be an incorporeal outsider with a possession ability similiar to the ghost.
Dabus: the manitainers of Sigil who spoke with visual puzzles. Might make sense to expand their duties tp places elsewhere as well.
Dark Dwellers: troll-like humanoids who are intelligent and regimented, and live beneath the earth
Demarax: A lizard-like creature with hundreds of tiny crystals embedded in its dark hide. The demarax roams slowly across the outer planes feeding on the spell crystals that are the manifestation of summoning spells in the planes. Highly magic resistant, demaraxes are usually non-hostile, but can defend themselves with their tails, by shooting magic missiles from their three eyes, or by releasing a storm of spell crystals. Although pretty dumb, Demaraxes live for thousands of years and can perfectly recall every conversation they've ever had, making them a potential source of information for planar adventurers
Gargouille: Aquatic dragon that breaths water
Garmorm: A vast floating worm native to the Astral Plane, the garmorm absorbs creatures into it with a song - creatures that fail to resist have their soul swallowed and join the choir of faces that cover its body. They are also accomplished spellcasters from all the souls they've absorbed over the centuries, and have a powerful bite.
Gautiere: the deicide cursed remnants of the Tiere, bottled up within Minethys on Carceri
Golem, Nyraala: the nyraala golem is an illithid creation of flesh and psionically active mucous. I've been hoping to see it in 3E at some point, since you can never have too many tentacle monsters.
Hai Riyo: also known as a dragon bird, this inhabitant of Kara-Tur appears to be a massive bird, even larger than a roc, but with the bewhiskered head of an oriental dragon. Its metallic-seeming feathers look almost like scales of copper and are harder than normal feathers. It can breathe a cone of scalding steam, can swallow whole, and possesses air-related abilities and immunities. It is an extremely silent hunter, able to drop down and suprise adversaries, despite its size.
Molian Heart: A disembodied human heart trailing arteries and veins in a sinister tangle. These undead creations of the necromancer Drake of the Black Academy of Moil remain inanimate until a living creature approaches. Then they drain life force and begin beating, animating those that they kill as Moil zombies (bleakborn in Libris Mortis). Although a molian heart has no physical attacks, it can project a wave of frost at neaby enemies.
Linqua: Linqua are the servitors of Sung Chiang, the god of theives from a Chinese mythos. Short squat humanoids tufted with green hair, they recieve the blessings of their creator in clerical spells, the ability to gain a burst of Strength (rather like the Strength domain power) and sneak attack. Despite their divine origin, linquas often escape the service of their master. These rogue linquas often make for powerful clerics, as they become addicted to the divine energy imbued by serving a god.
Living Hair: An manifestation of vanity, living hair forms when a person weaves a carpet or curtain out of their own hair, incorporating mystic runes into the designs. They despise all life, and dwell in the castles and manors of their creators (often after killing them). They strangle opponents in their fibrous mass, can ooze through tiny holes, and can only be killed with fire.
Magenta's Cat: psionic cats
Mapmaker: odd humanoids from Pandemonium who love maps
Mole Dragon: Wicked dragonets related to the pseudodragon, mole dragons have thick bodies and short tails. Their claws are huge and adapted to digging through earth and stone, and its hide is encrusted with gemstones. They have no breath weapon, but can summon earth elementals and cast spells as a cleric. They occasionally cooperate with derro and duergar and tend to be dour and sadistic.
Mortiss: Mortiss are a colony of coral-like worms that infest ships. They can burrow through wood and stone and will eventually destroy a ship's hull. A colony of Mortiss usually defends itself using their head spines, which contain a strong delusion-inducing poison. They can also lunge and latch onto a victim with their jaws. Although originally designed with spelljamming craft in mind, Mortiss could be easily adapted to Eberron's airships, or even water-going craft.
Murdrakus: Creations of the Boneheart of Iuz, the murdrakus is a two headed draconic creature ninety feet long. It breathes lines of fire, and is so hot that merely touching the creature deals fire damage. Its tail can sever limbs on a successful critical hit. It regenerates rapidly, but can be permanently slain with acid and negative energy.
Ni'iath: Long, wormlike creatures with vicious mouths and four narrow eyes spaced equidistantly about their heads. Natives of Bytopia, ni'iaths have a peculiar immunity to gravity and no concept of "up" or "down". They have a barbed tail and a special reverse gravity fling they use to propel opponents into nearby objects. Ni'iaths resemble wolves in mentality, hunting in packs, often tiring prey out before closing to attack.
Peluda: a dragonlike creature with a long neck and tail, no wings, four feet like those of a giant snapping turtle, and a back covered with bright orange quills. The base of these quills is pine green. A peluda's body is turtleshaped but without a shell, and the quills and coarse fur give the torso a shaggy appearance. Its venomous quills provide protection against attacks and can be flung as ranged weapons. It can also change its coloration to provide camouflage.
Poltergeist: Not the same as the poltergeist from the 1e Fiend Folio, but the spirits of chaotic gnomes from Limbo and Gladsheim (Ysgard), I guess they would be greater poltergeists
Quatsch: Skull-faced monkey that causes confusion
Rohch: The rohch is an unspeakable (or at least unpronounceable) crossbreed between a beetle and a wolf. Creepy things.
Rummele: Extraplanar dog with magical powers (including the ability to take human form --- which would make it the good counterpart to the canomorphs)
Scathe: Hairless, milky-white humanoids, with thin membranes joining their limbs, and a thick tail. Scathes use their long, curved claws as ice skates, and their membranes as sails to skate across desolate arctic plains. Difficult to detect, scathes hunt in packs, attacking with claws, a poison beak attack, and -- according to the picture at least -- a bladed mace. They communicate in howls and shrieks often mistaken for the arctic winds.
Tunnelmouth Dweller: I think this one has some of that old school, Gygaxian spirit in that it's a monster that doesn't really make sense anywhere outside of a dungeon. Basically, it's got a huge mouth, which it keeps open, blocking the entire dungeon. Then it waits for something to walk in.
Viltch: hateful vandals from the plane of Pandemonium, they resemble 3-legged dirty-gray mandrills. They have fiendish powers and immunites as well as roguelike skills and evasion. They can also dodge ranged attacks. Viltches prefer acts of hooliganism to actual killing.
Wastrels: life sucking, raven-like birds from the Gray Waste
Wraithworm: Giant snake that can become incorporeal and drain levels