Yeast
In the files, a folder named yeast can be found. It contains a huge collection of various enemy and boss ideas. These ideas merely exist as sprites or drawings, and while not currently planned to be added, that does not mean some ideas will never be added.
The following are almost all of the images that can be found inside the folder:
Sprites
Agateway
This enemy actually has an entire animation file that shows us that this enemy would have been able to teleport around the room.
Amfy
Angler
Not to be confused by the unused enemy with the same name.
Ballooner
What seems to be a womb variant of a Melty.
Baloon
Bang
Battering
Blaster Knight
This variant of Knights, according to its spritesheet, was supposed to launch its brain, probably aiming at the player, similar to how Chaser does it.
Bloodin
Bony Balor
Bony Morsel
Bony Worms
Bore
An unknown enemy with an unfinished sprite.
Buff Ghost
A pair of enemies that, according to concept art, would have the left one be sent out by the right one in order to rapidly punch Isaac.
Butt Grimace
A Grimace variant that would probably release poison gas clouds similarly to Gasbag.
Cadre
Cadre resembles a Grub or Larry Jr. made out of Globins. It probably would have Grub's AI and it would split into Globins and Gazing Globins, similarly to Globscraper, upon death. It is assumed Cadre would be found mostly in chapter 4.
Cannonball
A pair of enemies with unknown behavior. It is possible that the enemy on the right launched the enemy on the left at the player.
Chaff
Charcoal
Chomp
Chomp seems to be an early version of the Gamper, with both clearly resembling the Chain-Chomp enemy from Mario.
Daddy Haunt
Dandruff
Decoy Boy
Devious Dip
Dimwit
An unknown enemy. Its body sprites may have been modified and reused for the Missing Link.
Double Crosser
What seems to be a holy variant of Woodburner.
Dust Bunnies
Enemies that appear similar to the ones found in Super Meat Boy.
Edmund Sketch
Egg Practice
Explode Forever
Eyesore
Fat
Fistula Boys
Fun Guy
Geomancer
Glimdark
Gnaw
Goat Boy
Greed
A few greed-themed enemies, possibly meant to be enemy reskins for Greed Mode.
Guy
Headcase
What seems to be a tainted Mr. Horf.
Heartbeat
What looks like a fatty verson of Punted.
Hells Janitor
Home
Homing Priest
Hydro Knight
A Knight variant which, judging by the name, would appear in either Downpour or Flooded Caves.
IQ Baby
Jelly Shroom
Knife Brim
A Vis variant that would possibly function like the synergy of Mom's Knife and Brimstone.
Knight Slammer
Possibly an earlier version of the Thwammy due to its size.
Liberty
Lil Jugg
Loomer
An enemy that looks like it would have appeared in Gehenna. It also bears a resemblance to Hangman.
Max
Meaty Bone
An enemy that looks like a floating Clotty or Meatwad.
Megaton
A bigger version of the earlier Bang.
Mistmonger Hard Mode
Judging by the name, this enemy would have probably been a tainted, or at least harder, version of the Mistmonger.
Mutant Hive
Necro
Oracle Box
An enemy that might have appeared in Psionic Sheol.
Paunch
What appears to be a boss version of Roly Polies.
Poop Globin
Popcorn Fly
Popup Gaper
Potato Bag
Preserver
Quickerspirit
Based off the enemy's name, would've most likely made other enemies faster.
Receptor
Red Squirt
Possibly an early version of the Berry enemy.
Revelations Snaggers
Enemies that look like Snagger variants which would likely appear on the Revelations floors Glacier and Tomb.
Ringer
Robunculus
Sausage Roll
An enemy that seems to be a Roly Poly variant of the Fistuloid.
Seared Gaper
A Gaper variant that might have appeared in Smoky Burning Basement.
Shark Worm
An enemy that might have appeared in either Downpour or Flooded Caves, the latter being more likely.
Sirloin
Snarler
Spider Turret
Sporax
Spore Cannon
Squeaky
Squeaky is what seems to be an early version of Sponge.
Stitch
Submariner
An enemy that might have appeared in either Downpour or Flooded Caves; they have several skins, suggesting they might have appeared in both.
Tender Loin
A smaller version of the above Sirloins.
Tetris
An I, O, L, and S block made from Wimpies, the bottom wimpies resembling Stompies.
Tishooter
Vom
Wet
Two enemies that may have been earlier versions of the Mayfly and Mightfly.
Wrinkly
A very strange enemy that may have appeared in Scarred Womb.
Drawings
Ashen Bony
Big Burbly
Braniac
What was originally a mobile version of Glass Eye.
Brander
Gulper
A Cellar boss concept.
Crimson Court
Deep Dweller
Duke of Hazards
Fistulo
Gump
Inkert
Matriarch Glitch
Mine Worm
Mor-tar
Not Kingpin
Possibly an older version of Buck, whose name would have originally been 'Kingpin'.
Oldest Concepts
A bunch of drawings of early FF enemy concepts, including some which have never been seen.
Painter
Slammo
Possibly meant to be the boss version of a Slammer.
Succubus
Targeists
Zombie Air Unit
An enemy that, according to the Devs[1], was 'pitched seriously' at one point. Its behavior is unknown.