Thelric has an exhaustive list of everything in the game and expansions. This post is just meant to break out the Monsters only since they do not have the expansion symbol. This is probably the most asked question when it comes to components so I felt it needed its own entry so it could be clearly linked to without wading through the other info. This list is broken out by expansion since the question usually comes up in regards to separating out expansions.

Arkham Horror
x3 Byakhee - Blue
x2 Chthonian - Green
x6 Cultist - Black
x3 Dark Young - Yellow
x1 Dhole - Black
x2 Dimensional Shambler - Red
x2 Elder Thing - Black
x2 Fire Vampire - Blue
x1 Flying Polyp - Blue
x2 Formless Spawn - Black
x3 Ghost - Yellow
x3 Ghoul - Black
x1 God of the Bloody Tongue - Black - Mask
x2 Gug - Black
x1 Haunter of the Dark - Blue - Mask
x1 High Priest - Black
x2 Hound of Tindalos - Green
x3 Maniac - Black
x3 Mi-Go - Blue
x2 Nightgaunt - Blue
x2 Shoggoth - Red
x2 Star Spawn - Black
x1 The Black Man - Black - Mask
x1 The Bloated Woman - Black - Mask
x1 The Dark Pharaoh - Black - Mask
x1 Vampire - Black
x2 Warlock - Yellow
x2 Witch - Black
x3 Zombie - Black

Dunwich Horror
x3 Child of Abhoth - Purple - Spawn
x2 Colour Out of Space - Green
x1 Cultist - Black
x1 Dark Young - Yellow
x1 Formless Spawn - Black
x2 Goat Spawn - Red
x1 Hunting Horror - Green
x1 Mummy - Purple
x2 Rat-thing - Purple
x5 Servant of Glaaki - Black - Spawn
x1 Spectral Hunter - Yellow
x1 Star Vampire - Purple
x2 Tcho-tcho - Black
x1 The Beast - Purple - Mask
x1 The Dunwich Horror - Green - Spawn
x1 Wizard Whateley - Black
x2 Wraith - Blue

King in Yellow
x3 Riot - Black - Spawn

Kingsport Horror
x3 Crawling One - Black
x1 Cultist - Black
x1 Formless Spawn - Black
x1 Ghast - Black
x1 Gnoph-Keh - Black
x4 Leng Spider - Black
x2 Moon-beast - Orange
x2 Nightgaunt - Blue
x3 Serpent People - Black
x1 Shadowy Figure - Green - Mask
x2 Shan - Blue
x2 Skeleton - Orange
x1 Tcho-tcho Priest - Red
x1 The Skinless One - Red - Mask
x1 Werewolf - Green
x2 Yithian - Black

Black Goat of the Woods
x3 Child of the Goat - Black
x1 Dark Druid - Green
x3 Dark Young - Yellow
x2 Goat Spawn - Red

It might be worth noting which monsters are Spawns / Masks too, as not all monsters are added to the cup.

Innsmouth Horror

x1 Barnabas Marsh - Orange
x4 Being of Ib - White - Spawn
x1 Cultist - Black
x6 Deep One - Orange
x4 Deep One Hybrid - Orange
x1 Elder Thing - Black
x3 Lloigor - Green
x1 Mi-Go - Blue
x1 Priest of Dagon - Orange
x4 Proto-Shoggoth - Red
x1 Tendril of Nyogtha - Black - Spawn
x1 Servitor of the Outer Gods - Blue
x2 Shoggoth - Red
x1 Shugeron - Orange - Mask
x1 Wailing Writher - Yellow - Mask

I wish they had printed the symbol from the set the monster came from on the tokens. They did it for all the cards and it would have made it easier to play with the version you want. If say you wantedto play with just the base set and one or two others.

WB

William Blake said:

If you mark the sides of the monster tokens for each expansion with a different colour that might work. Easy to sort out and during play, if they are in the monster cup, you don't see it.

I just went through a count of Masks and non-Spawn monsters (up to and including Innsmouth). It's 144. So... 134 without masks. Someone might find this useful for calculating chances for monster draws.