I put this together to stop rooting through 40 issues when I'm looking for something. I don't have Rise of the Runelords, and if this makes Paizo angry, feel free to delete. Monsters that were reprinted/updated in Bestiary 2 aren't listed.
7 Edge of Anarchy
Harrow (The Harrow Deck)
People of the Road (Varisians)
Bestiary:
Dream Spider (1/2 Vermin)
Raktavarna (3 Outsider)
8 Seven Days to the Grave
Plague and Pestilence (Diseases)
Abadar
Bestiary:
Daughter of Urgathoa
Lawgiver (15 Construct)
Nosferatu
9 Escape from Old Korvosa
Faces of the Earthbound Evils (Rakshasas)
The Red Mantis
Bestiary:
Achaekek, The Mantis God (30 Outsider)
Beatific One (9 Outsider)
Rajput Ambari (7 Undead)
Rakshasa Maharajah (18 Outsider)
Sikari Macaque Swarm (5 Animal)
10 A History of Ashes
The Cinderlands
People of the Storval Plateau (Shoanti)
Bestiary:
Bonestorm (8 Undead)
Cinder Wolf (2 Magical Beast)
Havero (24 Aberration)
Red Reaver (13 Mag Beast)
11 Skeletons of Scarwall
The Hold of Belkzen
Zon-Kuthon
Bestiary:
Chained Spirit (14 Undead)
Danse Macabre (14 Undead)
The Prince in Chains (15 Outsider)
12 Crown of Fangs
Relics of Kazavon
Harrow Deck of Many Things
Bestiary:
Akaruzug (14 Construct)
Contract Devil, Phistophilus (10 Outsider)
Mobogo (10 Mag Beast)
13 Shadow in the Sky
Riddleport: City of Cyphers
The Gold Goblin (Casino)
Bestiary:
Darklands Sentinel (2 Mag Beast)
Fungal Crawler (3 Aberration)
14 Children of the Void
Into the Black
Cayden Cailean
Bestiary:
Void Zombie
Thais (15 Outsider)
15 The Armageddon Echo
Celwynvian
Drow of Golarion
Bestiary:
Blast Shadow (5 Undead)
Cutlass Spider (6 Construct)
Maftet (6 Mon Humanoid)
16 Endless Night
Zirnakaynin
Abominations of the Drow
Bestiary:
Deep Crow (14 Mag Beast)
Ghonhatine (10 Aberration)
Irnakurse (9 Aberration)
17 A Memory of Darkness
Kyonin
Calistria
Bestiary:
Menotherian (15 Outsider)
Treerazer, Lord of the Blasted Tarn (25 Outsider)
18 Descent into Midnight
The Land of Black Blood
Demon Lords of Golarion
Eando Kline
Bestiary:
Black-Blooded Template
Xacarba (15 Outsider)
19 Howl of the Carrion King
Gnolls of the Brazen Peaks
Bestiary:
Div, Doru (2 Outsider)
20 House of the Beast
In the Shadow of Pale Mountain
Sarenrae
Bestiary:
Buraq (5 Magic Beast)
Edimmu (3 Undead)
Div, Pairaka (7 Outsider)
Sunlord Thalachos (15 Outsider)
Unchosen Gnoll (4 Humanoid)
21 The Jackal's Price
Tales and Truths of Genies
The Katapesh Marketplace
Bestiary:
Div, Shir (10 Outsider)
Emkrah (9 Aberration)
Hadhayosh (18 Mag Beast)
Rukh (10 Animal)
Tophet (10 Construct)
22 The End of Eternity
The Seals of Sulesh the Great (Conjuring/Binding Genies)
Keepers of Chaos (Proteans)
Bestiary:
Coeurl (8 Mag Beast)
Miengu (11 Fey)
23 The Impossible Eye
The City of Brass
Rovagug
Bestiary:
Black Jinni (12, outsider)
Div, Sepid (14, outsider)
Get of Iblis (13, aberration)
Nephilim (8, Outsider)
24 The Final Wish
Spawn of Rovagug
Wishcraft
Bestiary:
Ahriman (22, outsider)
Azi, Gandareva (16, dragon)
Azi,Srurava (15, dragon)
Azi, Zahhak (19, Dragon)
Golem, Brass (14, Construct)
Simurgh (18, Mag Beast)
Xotani the Firebleeder (20, Mag Beast)
25 The Bastards of Erebus
Westcrown
Tieflings of Golarion
Bestiary:
Gremlin, Haniver (1/2 fey)
Rot Grub (7 vermin swarm)
Giant Rot Grub (3, vermin)
Shadowgarm (2, aberration)
Strix (1/3 Mon Humanoid)
Torble (1/8 Vermin)
Torble swarm (2 vermin)
Devil, Ukobach (4 Outsider)
26 The Sixfold Trial
The Six Trials of Lazarod (play)
Iomedae
Bestiary:
Devil, Salikotal (7, Outsider)
Graveknight (11, undead)
Hand of the Inheritor (15 Outsider)
Stymphalides Swarm (6 Mag Beast)
Giant Stymphalides (8 Mag Beast)
27 What Lies in Dust
Treasures of the Pathfinders
Hellknights
Bestiary:
Aspidolechone (17 Mag Beast)
Devil, Chortov (9 Outsider)
Idol, Bone (2 Construct)
Idol, Jade (4 Construct)
Idol, Wood (1 Construct)
Idol, Stone (3 Construct)
Lar (5 Outsider)
Naga, Royal (11 Aberration)
28 The Infernal Syndrome
In the Fiend's Grasp (Possession)
Path of the Hellknight
Bestiary:
Asura, Adhukait (7 Outsider)
Cerberi (6 Outsider)
Malbolgian Cerberi (12 Outsider)
Devil, Cabal (Uniila)(10 Outsider)
Spartolos (6 Undead)
29 Mother of Flies
Ecology of the Thieves' Guild
Asmodeus
Bestiary:
Basileus (15 Outsider)
Calikang (12 Mon Humanoid)
Devil, Possession (Gidim)
Lesser Gidim (6 Outsider)
Greater Gidim (15 Outsider)
Nihiloi (11 Outsider)
Vrykolakas (10 Undead)
30 The Twice-Damned Prince
Catastrophe!
Mammon
Bestiary:
Devil, Advodaza (18 Outsider)
Ebon Acolytus (7 Construct)
Gigas, Hell (15 Humanoid)
Kyton, Ephialtes (16 Outsider)
Vouivre (12 Mon Humanoid)
31 Stolen Land
Into the Wild
Brevoy
Bestiary:
Carbuncle (1 Mag Beast)
Drekavac (3 Undead)
Elk (1 Animal)
River Elk (2 Animal)
Megaloceros (4 Animal)
Tatzlwyrm (2 Dragon)
Thawn (2 Humanoid)
Thylacine (1/2 Animal)
Brush Thylacine (2 Animal)
32 Rivers Run Red
Of Cities and Kings (City-Building)
Erastil
Bestiary:
Ceratiodi (3 Mon Humanoid)
The Grim White Stag (15 Outsider)
Hodag (5 Mag Beast)
Rorkoun (6 Aberration)
Trollhound (3 Mag Beast)
33 The Varnhold Vanishing
Iobaria Gazeteer
Into the Stolen Lands
Bestiary:
Blodeuwedd (6 Fey)
Clawbat (1 Mag Beast)
Cyclops, Great (12 Humanoid)
Peluda (10 Dragon)
Stygiria (7 Mon Humanoid)
34 Blood for Blood
Ecology of the Boggard
The Spoils of Kings
Bestiary:
Ahuizotl (6 Mag Beast)
Bog Strider (2 Mon Humanoid)
Calathgar (4 Plant)
Leshy, Fungus (2 Plant)
Nuckelavee (9 Fey)
35 War of the River Kings
Pitax
Gorum
Bestiary:
First Blade (15 Outsider)
Irlgaunt (13 Aberration)
Verdurous Ooze (6 Ooze)
Greater Verdurous Ooze (11 Ooze)
Warsworn (16 Undead)
36 Sound of a Thousand Screams
Beyond Kingmaker
The First World
Bestiary:
Ankou (14 Fey)
Dweomercat Cub (2 Mag Beast)
Dweomercat (7 Mag Beast)
Grodair (5 Mag Beast)
Skrik Nettle (6 Mag Beast)
Zomok (16 Plant)
37 Souls for Smuggler's Shiv
Shipwrecked!
Ecology of the Serpentfolk
Bestiary:
Ochre Eurypterid (1/3 Vermin)
Common Eurypterid (1 Vermin)
Bluetip Eurypterid (5 Vermin)
Spiny Eurypterid (9 Vermin)
Spitting Eurypterid (12 Vermin)
Ningyo (1 Mon Humanoid)
Undead Ningyo (1 Undead)
Rhamphorhynchus (1/3 Animal)
Dimorphodon (1 Animal)
Quetzalcoatlus (7 Animal)
Hunter Urchin (1 Vermin)
Spear Urchin (4 Vermin)
Glass Urchin (9 Vermin)
Tuyewera (4 Undead)
38 Racing to Ruin
Eleder
Gozreh
Bestiary:
Adaro (3 Mon Humanoid)
Biloko (1/2 Fey)
Bloodhaze Mosquito Swarm (6 Vermin)
Chemosit (4 Mag Beast)
Personification of Fury (15 Outsider)
39 City of Seven Spears
Expedition to Saventh-Yhi
The Path of Juju
Bestiary:
Camulatz (9 Mag Beast)
Snake Swarm (2 Animal)
Venomous Snake Swarm (4 Animal)
Piranha Swarm (3 Animal)
Megapiranha Swarm (6 Animal)
Vireseed Swarm (5 Plant)
Mokele-Mbembe (9 Animal)
Tribal Totem (6 Construct)
Umasi (4 Mon Humanoid)
40 Vaults of Madness
Ecology of the Charau-Ka
Dungeon Deathtraps
Bestiary:
Impundulu (11 Outsider)
Obambo (13 Undead)
Popobala (15 Mon Humanoid)
Sabosan (5 Mon Humanoid)
Tikoloshe (3 Undead)
41 The Thousand Fangs Below
Ilmurea
Nethys
Bestiary:
Arcanotheign (15 Outsider)
Inkanyamba (13 Mag Beast)
Lukwata (11 Mag Beast)
Umbdhlebi (12 Plant)
42 Sanctum of the Serpent God
Beyond Serpent's Skull
Ydersius
Bestiary:
Baregara (12 Outsider)
Emperor of Scales (15 Outsider)
Grootslang (16 Mag Beast)
Hollow Serpent (16 Undead)
Lesser Hollow Serpent (6 Undead)
Kongamato (15 Dragon)
43 The Haunting of Harrowstone
Ravengro
Haunts
Bestiary:
Sanguine Ooze Swarm (1/3 Ooze)
Phlegmatic Ooze Swarm (1/2 Ooze)
Melancholic Ooze Swarm (1 Ooze)
Choleric Ooze Swarm (2 Ooze)
Animated Manacles (1 Construct)
Animated Jack-O-Lantern (2 Construct)
Animated Straitjacket (4 Construct)
Severed Head (1/3 Undead)
Flaming Skull (1/2 Undead)
Skull Swarm (1 Undead)
Giant Beheaded (2 Undead)
Medusa Head (3 Undead)
Changeling (1/2 Humanoid)
Ectoplasmic Template
Spring-Heeled Jack (3 Fey)
44 Trial of the Beast
Pharasma
Esoteric Order of the Palatine Eye
Bestiary:
Boruta (9 Plant)
Skin Stealer (2 Fey)
Steward of the Skein (15 Outsider)
Four-Armed Mudra Skeleton (1/2 Undead)
Skeletal Mount (1 Undead)
Armored Ogre Skeleton (2 Undead)
Skeletal Mage (5 Undead)
Multiplying T-Rex Skeleton (9 Undead)
45 Broken Moon
The Whispering Way
Ecology of the Lycanthrope
Bestiary:
Vilkacis (7 Undead)
Weaverworm (8 Aberration)
Werebat (Human Form) (3 Humanoid)
Werebat (Hybrid Form) (3 Humanoid)
Zombie Wolf (1 Undead)
Apocalypse Zombie (2 Undead)
Giant Zombie (8 Undead)
Zombie Lord (3 Undead)
Several of these have been updated in the Pathfinder World Guide: Inner Sea.
Daughter of Urgathoa, Calikang, Strix, Treerazer that I can recall.
In addition, I believe the Beatific One is updated in the Cult of the Ebon Destroyers module.