• Crucified

Found once at the very beginning of the game.

• Undead
  
• Roach
  
• Blue Eye
  
• Imp
  
• Banshee

All of the above are found in Darsov Shire and several other locations during day or night.

• Specter

Mini-boss in a house in Arkos when choosing the "Never" option when asked to blow up the dam.

• Red Eye

Found all over the place.

• Skeleton-S
  
• Skeleton-L
  
• Skeleton-A
  
• Deadknight

All of the above can be found in the Darsov Shire dungeon among other places.

• Horned-S
  
• Horned-L
  
• Horned-A
  
• Eyelord

All of the above can be found in several of the main dungeons.

• Deep One

Deep One is exclusive to the Stormheim Shore dungeon.

• Sorcerer
  
• Wizard
  
• Warlock

Mainly found in the Mount Kastka dungeon.

• HellFetus
  
• Putrid-S
  
• Putrid-A
  
• Putrid-L

Mainly found in the Kadjanto Peak dungeon.

• Fallen
  
• Cursed-L
  
• Cursed-A
  
• Cursed-S
  
• Gargoyle

Can only be found in the dungeon exclusive to the Ultimate Good ending.

• Corrupted
  
• Fanatic

Can only be found in the bonus dungeon exclusive to the Future ending.

• Nightmare

Can only be found in the Dreamscape, which you access from a quest in Kastski.

• Vile Knight
  
• Great Imp

Can only be found in the extra mini-dungeon in Stormheim Shore.

• Bat

Exclusive to the last boss encounter of the Ultimate Good ending (AFAIK).

• CageDemon

Found immediately east of Arkos, only during the night. Not 100% sure if you need to pick a specific option in order for its entry to be added, since you can kill him both ways.

• Necro

Mini-boss of the barn quest that you can get in Darsov.

• NightFiend
  
• NightBeast

Only encountered at night in various places on the overworld.

• Remus

Can only be encountered during a quest in Kastski where you're asked to get rid of a skeleton, need to pick the Slay option.

• Cultist-A
  
• Cultist-S
  
• Cultist-L
  
• Worshipper
  
• HighPriest

Cultists are encountered on many occasions, mostly when doing a Good or Ultimate Good playthrough, Lancers seem to be very rare (I only have two kills) so they are probably exclusive to the late quests during those routes. HighPriests are exclusive to those late game Ultimate Good quests.

• Guard-S
  
• Guard-A
  
• Guard-L
  
• Sergeant-A
  
• Sergeant-S
  
• Captain
  
• Tancred

All of the above are killable during the final quests when doing an Ultimate Evil playthrough.

• Robert

Exclusive to the Ultimate Evil route, need to choose the Kill option near the end of the route (Other option gives a bonus ending).

• Goon

Exclusive to the Good or Ultimate Good routes, one per playthrough.

• Priest

Killable during the final quest when doing an Ultimate Evil playthrough.

• Hans

Killable during an Evil or Ultimate Evil route, you will be asked to kill him for an early Evil quest and you will have to choose to do it to confirm the kill.

• Edgar

Exclusive to the Ultimate Evil route, will die as part of the last quest for that route (IIRC).

• Possessed

The possessed priest that you will be asked to find an exorcist for. You can attack him while he's hovering.

• UrzonCult

Killable in the Urzon Citadel when doing a Good or Ultimate Good playthrough.

• Mage

Will be killed as part of a quest during an Ultimate Good playthrough.

• Scorpion (EASY TO MISS)

The ballista that can only be found in a specific hallway that is only accessible at the end of the Ultimate Evil playthrough, needs to be destroyed in addition to the guard manning it.

• Horseman

Mini-boss exclusive to the end quests of the Ultimate Evil route.

• Werewolf

Can be attacked at night, found at the East of the Darsov Shire, will have to be killed in order to get to Gregor.

• Skeleton Knight

Mini-boss of a quest in Darsov where you're asked by the inn keeper to kill the monster attacking the grave of a relative.

• Aberration

Killed as part of the mandatory starting quest.

• Brutus

Only killable if you chose to "Slay" Remus earlier as part of a quest in Kastski, will appear close to the Kadjanto Peak dungeon.

• Armored Aberration

Will die as part of a quest exclusive to the Ultimate Good route where you need to defend Darsov. You might need to actually hit it for it count in the compendium, even though you're technically not killing it yourself.

• Champion of Rot
  
• Bubonic Aberration

Both are found in the Kadjanto Peak dungeon.

• Biomechanical Horror

Killable in the bonus dungeon exclusive to the Future ending.

• Tormentor
  
• Unholy Abomination

Killable in the dungeon exclusive to the Ultimate Good route.

• Crypt Skeleton

Found in the bonus mini-dungeon in the Combbelton Cemetery, need to be on the Ultimate Good or Evil routes.

• Halphas

Boss of the bonus Stormheim Shore mini-dungeon.

• Faceless One (EASY TO MISS)

Answer "Never" to the hermit in the lone house in the shores of Upel, that is only accessible during the day.

• Lord of Maggot

Boss of the bonus Combbelton Cemetery mini-dungeon.

• Mammon

Boss found in Danielle's basement in Valeshire where you learn the downward attack.

• Corrupter of Mind
  
• Champion of Hell
  
• Hell Cherub
  
• Hell Monarch
  
• Ancient Wurm
  
• Baron of Decay

All of the above are found in the dungeon exclusive to the Ultimate Good ending.

• Paimon

At the beginning of the game, try to help the man who asks you to kill him.

• Mahalmon

Boss of the Darsov Shire main dungeon.

• Kalamon

Boss of the Combbelton Cemetery main dungeon.

• Leviathan

Boss of the Stormheim Shore main dungeon.

• Apollyon

Boss of the Mount Katska main dungeon.

• Alastor

Boss of the Kadjanto Peak main dungeon.

• Azazel

Boss of the Future ending.

• Crocell

Boss of the Dreamscape mini-dungeon, only accessible during a quest in Kastski that requires an elixir.

• Paimon True Form

Only killable if you fought Paimon earlier, and with a quest from Arkos.

• Belphegor

End boss of the Good or Evil routes.

• Baphomet

End boss of the Ultimate Good route.

• Abbadon

End boss of the Ultimate Evil route.