Let's see, it's probably easier if I list the monsters I haven't used.
MM 3.5:
Aboleth Mage
Achaierai
Allip
Ankheg
Aranea
Archon, Hound Hero
Arrowhawk, Juvenile
Assassin Vine
Basilisk, Abyssal Greater
Blink Dog
Centaur
Cloaker
Cockatrice
Darkmantle
Delver
Destrachan
Digester
Dinosaur, Deinonychus
Dinosaur, Elasmosaurus
Dinosaur, Megaraptor
Dire Shark
Displacer Beast Pack Lord
Doppelganger
Dragonne
Dryad
Ethereal Filcher
Ethereal Marauder
Formian, Myrmarch
Formian, Queen
Formian, Taskmaster
Formian, Warrior
Formian, Worker
Fungus, Violet
Genie, Janni
Giant, Cloud
Giant, Stone
Giant, Storm
Golem, Stone, Greater
Gorgon
Grick
Hag, Sea
Halfling
Harpy
Harpy Archer
Hell Hound, Nessian Warhound
Homunculus
Invisible Stalker
Krenshar
Kuo-toa
Lamia
Lammasu
Lammasu, Golden Protector
Locathah
Magmin
Manticore
Mephit, Dust
Mephit, Ice
Mephit, Ooze
Mephit, Salt
Mephit, Steam
Mephit, Water
Merfolk
Mimic
Mind Flayer Sorcerer
Naga, Dark
Naga, Guardian
Naga, Spirit
Naga, Water
Nightmare, Cauchemar
Ogre Barbarian
Ooze, Gelatinous Cube
Ooze, Ochre Jelly
Owl, Giant
Pegasus
Phantom Fungus
Phasm
Rust Monster
Sea Cat
Shadow, Greater
Shadow Mastiff
Shocker Lizard
Skeleton
Sphinx, Androsphinx
Sphinx, Criosphinx
Sphinx, Gynosphinx
Sphinx, Hieracosphinx
Spider Eater
Sprite, Nixie
Tarrasque
Titan
Tojanida, Adult
Tojanida, Elder
Tojanida, Juvenile
Triton
Troll Hunter
Umber Hulk, Truly Horrid
Unicorn, Celestial Charger
Vampire, Elite
Will-o'-wisp
Wraith, Dread
Xorn, Minor
Yeth Hound
FF:
Abrian
Aoa, Droplet
Aoa, Sphere
Aquatic Ooze, Flotsam Ooze
Bacchae
Blood Hawk
Bloodthorn
Canomorph, Haraknin
Canomorph, Shadurakul
Canomorph, Vultivor
Century Worm
Dark One, Dark Creeper
Dark One, Dark Stalker
Darkweaver
Death Dog
Disenchanter
Ethereal Ooze
Fensir
Fensir, Rakka
Feytouched
Flame Snake, Lesser
Flame Snake, Minor
Formian, Armadon
Formian, Observer
Formian, Winged Warrior
Fossergrim
Imp, Bloodbag
Imp, Euphoric
Imp, Filth
Indricothere
Iron Cobra
Jackal Lord
Jackalwere
Kelp Angler
Kelpie
Khaasta
Living Holocaust
Lucent Worm
Megatherium
Mongrelfolk
Necrophidius
Octopus Tree
Oread
Planetouched, Maeluth
Planetouched, Mechanatrix
Sarkrith, Spelleater
Sarkrith, Thane
Selkie
Senmurv
Shadow Asp
Shedu
Skulk
Spirit of the Air
Sporebat
Spriggan
Sunwyrm
Swarm, Cranium Rat, Average
Swarm, Cranium Rat, Greater
Swarm, Cranium Rat, Lesser
Swarm, Plague Ant
Swarm, Rapture Locust
Swarm, Scarab Beetle
Terlen
Terror Bird
Vine Horror
Vorr
Wicker Man
Yellow Musk Creeper
Yurian
Templates:
Half-Fey
Wendigo
Yellow Musk Zombie
MMII:
Abeil
Ash Rat
Asperi
Automaton, Hammerer
Automaton, Pulverizer
Blood Ape
Boggle
Bogun
Bone Naga
Bone Ooze
Braxat
Chaos Roc
Cloaked Ape
Clockwork Horror, Adamantine
Clockwork Horror, Electrum
Clockwork Horror, Gold
Clockwork Horror, Platinum
Cloud Ray
Corollax
Crimson Death
Desmodu
Desmodu Bat, Guard
Desmodu Bat, Hunting
Desmodu Bat, War
Dinosaur, Ankylosaurus
Dinosaur, Cryptocliudus
Dinosaur, Quetzalcoatus
Dinosaur, Seismosaurus
Dire Horse
Dragon, Gem, Amethyst
Dragon, Gem, Crystal
Dragon, Gem, Emerald
Dragon, Gem, Sapphire
Dragon, Gem, Topaz
Dread Guard
Dune Stalker
Ether Scarab
Ethereal Doppleganger
Ethereal Slayer
Felldrake, Crested
Felldrake, Horned
Felldrake, Spitting
Fire Bat
Flesh Jelly
Forest Sloth
Galeb Duhr
Gambol
Giant, Forest
Giant, Ocean
Glimmerskin
Golem, Stained Glass
Gravorg
Greenvise
Grimalkin
Grizzly Mastodon
Half-fiend, Durzagon
Immoth
Ixitxachitl, Average
Ixitxachitl, Vampiric
Jermlaine
Leechwalker
Legendary Ape
Legendary Bear
Legendary Eagle
Legendary Horse
Legendary Shark
Legendary Snake
Legendary Wolf
Linnorm, Dread
Loxo
Marrash
Meenlock
Megalodon
Moonbeast
Moonrat
Morkoth
Mudmaw
Myconid, Average Worker
Myconid, Circle Leader
Myconid, Elder Worker
Myconid, Guard
Myconid, Junior Worker
Myconid, Sovereign
Needlefolk
Nethersight Mastiff
Orcwort
Orcwort, Wortling
Ormyrr
Phase Wasp
Psurlon, Average
Psurlon, Elder
Psurlon, Giant
Raggamoffyn, Common
Raggamoffyn, Guttersnipe
Raggamoffyn, Shrapnyl
Raggamoffyn, Tatterdemanimal
Rampager
Reason Stealer
Red Sundew
Shadow Spider
Sirine
Spellgaunt
Spirit of the Land
Stone Spike
Swamplight Lynx
Sylph
Twig Blight
Windghost
Yak Folk
Templates:
Captured One
Half-Golem, Clay
Half-Golem, Flesh
Half-Golem, Iron
Half-Golem, Stone
I haven't worked the numbers, but I'm guessing I'm over 50%.
Some notes:
- I haven't used much of MMIII, mostly because I didn't find it terribly inspiring.
- Many of the monsters I haven't used I'd like to use -- they just haven't fit into one of the current campaigns or one-shots.
- Entire groups of creatures (formians, psurlons, etc.) haven't been used, but if I end up using one, I'll probably use most as I like "themed" encounters.
-I don't tend to use advanced monsters out of the books -- I prefer to advance them myself.
-I don't use sample templated monsters -- I make my own.