To add something to these list:
MC Mystara Appendix
Actaeon
Agarat
Ash Crawler
Baldandar
Bargda
Bhut --> Fiend Folio, although seems different
Bird, Magpie
Bird, Giant Magpie
Bird, Piranhabird (lesser & greater)
Bird, Sprackle (lesser & greater)
Blackball --> Epic Level Handbook
Brain Collector --> Epic Level Handbook
Chevall
Choker --> Monster Manual
Coltpixy
Crone of Chaos
Darkhood
Darkwing
Decapus --> Tome of Horrors
Deep Glaurant
Diabolus
Dragon, Crystalline
Dragon, Jade
Dragon, Onyx
Dragon, Ruby
Dragonfly (White, Black, Green, Blue, Red)
Drake, Mystaran (Mandrake, Wooddrake, Colddrake, Elemental Drake)
Dusanu
-->
Ebon Tiger
Elementals of Chaos (Air, Earth, Fire, Water)
Elementals of Law (Air, Earth, Fire, Water)
Familiars (Aryth, Bogan, Fylgar, Gretch, Ulzaq)
Frost Salamander --> Monster Manual 2
Fundamental (Air, Earth, Fire, Water)
Gargantua (carrion crawler, troll <-- kaiju template ?)
Geonid
Ghostly Horde
Giant, Athach --> Monster Manual (ironically, no more a giant)
Giant, Hephaeston
Golem, Amber
Golem, Drolem --> Monster Manual 2
Golem, Iron Gargoyle
Golem, Mud
Golem, Rock
Golem, Silver
Golem, Skeletal
Gray Philosopher
Guardian Horse
Guardian Warrior
Gyerian
Herex (Larva, Adult)
Hivebrood (Broodling, Soldier, Lieutenant, Mother, Controller)
Horde
Hsiao
Huptzeen
Hutakaan
Imp (Wood, Bog, Garden)
Jellyfish, Giant (Marauder, Death's hand, Galley)
Kna
Kopru --> Monster Manual 2
Living Statue (Crystal, Iron, Jade, Rock, Ooze, Silver, Steel)
Lizards (Draco, Giant Footpad, Giant Gecko, Giant Tuatara, Horned Chameleon, Lava, Rockhome, Xytar)
Lizard-kin (Cayman, Chameleon Man, Gator Man, Sis'thik)
Lupin
Lycanthrope, Werejaguar
Lycanthrope, Wereswine
Magen (Demos, Caldron, Galvan, Hypnos)
--> See there!
Manikin
Mek
Mujina
Nagpa
Nightshades (Nightcrawler, Nightwalker, Nightwing) --> Monster Manual
Nuckalavee
Pegataur
-->
Phanaton
Plant, Amber Lotus
Plant, Archer Bush --> Tome of Horrors
Plant, Grab Grass
Plant, Vampire Rose --> Tome of Horrors
Plasm (Normal, Giant)
Rakasta
Rock Man
Saberclaw
Sacrol
Scamille
Shapeshifter, Adaptor
Shapeshifter, Metamorph
Shapeshifter, Polymar
-->
Shapeshifter, Randara
Shargugh
Shark-kin
Sollux
Spectral Death
Spectral Hound
Spider-kin, Aranea --> Monster Manual
Spider-kin, Planar Spider
Spider-kin, Ploppéd
Spider-kin, Rhagodessa
Spirit, Druj
Spirit, Odic
Surtaki
Tabi
Thoul
-->
Thunderhead
Topi
Tortle
Vampire, Velya
White Fang
Worm (Great Annelid, Caecillia, Desert Leviathan, Fyrsnaca, Marine Leviathan, Red Worm, Slime Worm)
Wyrd (Lesser, Greater)
Yowler
Zombie, Lightning (Lesser, Greater)
I've converted four of them (the magens). I may do others if it interest anyone.