Canon Mystaran creatures in the 3.0 Monster Manual
by RipvanwormerAranea
Assassin vine - similar to strangle vine (Creature Catalogue)
Athach
Basilisk
Beholder
Blink dog
Bodak (similar to duskers in Talons of Night, vaguely)
Bugbear
Carrion crawler
Archon (Mystaran archons are very different, though)
Centaur
Chimera
Choker
Cockatrice
Demon (succubus, vrock, hezrou, glabrezu, nalfeshnee, marilith, and balor appear as whispering, screaming, croaking, howling, groaning, hissing, and roaring demons respectively)
Devil (imp only)
Dinosaur
Displacer beast
Doppelganger
Dragon
Dragon turtle
Dryad
Dwarf
Elemental
Elf
Fungus (shrieker)
Gargoyle
Genie (efreeti and djinni)
Ghoul
Giant (hill, stone, frost, fire, cloud, storm)
Giant eagle (as great eagle)
Giant owl (similar to hsiao)
Girallon (in Needle, though that's not explicitly Mystara it has Chak/planar spiders in it)
Gnoll
Gnome
Goblin
Golem
Gorgon
Griffon
Hag (crone of chaos)
Halfling
Harpy
Hell hound
Hippogriff
Hobgoblin
Homunculus (though Mystaran homunculi are different)
Invisible stalker
Kobold
Kraken
Lamia (as lamara)
Lammasu (on the Savage Coast)
Lizardfolk (as lizard man)
Manticore
Medusa
Merfolk (sometimes called merrow)
Mimic (polymar)
Minotaur
Mummy
Nightmare
Nightshade
Ogre
Ogre mage
Ooze
Orc
Owlbear
Pegasus
Phase spider (as planar spider)
Phasm (as scamille)
Rakshasa (as randara)
Roc
Roper
Rust monster
Sahuagin (in Blackmoor era as the Sar-Aigu; replace with shark-kin in Gazetteer era)
Salamander (as flame salamander)
Satyr (as faun)
Shadow (not undead in Mystara)
Skeleton
Spectre
Sphinx (only androsphinx and gynosphinx)
Sprite (nixie, pixie)
Stirge
Titan
Treant
Triton
Troglodyte
Troll
Umber hulk (as hulker)
Unicorn
Vampire
Wight
Will-o'-wisp (wychglow)
Winter wolf (ice wolf)
Wraith
Wyvern
Yeth hound (yowler)
Zombie
Monster Manual II
Automaton (as gnomish inventions or Blackmoor-era technology)
Catoplepas (as nekrozon)
Dinosaur (on the Isle of Dread and Hollow World)
Dire elk (as giant elk, found on the Isle of Dread)
Gem dragon (Mystaran gem dragons are different, though)
Golem, Stained Glass (similar to glassine horror in Savage Coast Monstrous Compendium)
Water weird (though very different)
Fihyr (native to the Demiplane of Nightmares according to Mystara Monstrous Compendium)
Frost salamander
Juggernaut (appears in Savage Coast Monstrous Compendium as Hulean juggernaut)
Ocean giant (as sea giant)
Mountain giant
Dragonflesh golem (as drolem)
Hook horror (as hook beast)
Ixitxachitl (as devilfish)
Kopru
Leviathan (a kind of worm in Mystara)
Loxo (similar to pachydermion)
Nimblewright (as clockwork swordsman)
Orcwort (similar to killer tree)
Ormyrr (similar to wurmling)
Phoenix
Spirit of the Land (spirits in Ethengar)
Thri-kreen (Savage Coast, possibly)
Scorpionfolk (as manscorpion)
Fiend Folio
Bhut (very different in Mystara)
Demodand (Savage Coast Monstrous Compendium confirms Carceri exists, anyway)
Half-fey (changelings?)
Half-troll (in the Broken Lands)
Indricothere (grangeri, on the Isle of Dread)
Maelephant (suggested in Mystara Monstrous Compendium as stand-in for malfera)
Megatherium (on Isle of Dread)
Sea drake (as sea serpent)
Shedu (on Savage Coast)
Terror bird (axe beak, on the Isle of Dread)
Monster Manual III
Goatfolk (as goatman)
Petal (similar to flitterling)
Phoelarch (implied by existence of phoenix?)
Redcap