Spoilers, duh

EDIT: I updated and fixed the list, sorted by area etc.pp. (thanks @ /u/SamLikesJam), so numbers are not what they were.

Ashina Outskirts:

1. First General Guy after second bonfire. Also drops a Gourd Seed.

2. The chained Ogre on the stairs after the next bonfire. Not optional.

3. The second General Guy. After the Ogre, surrounded by normal dudes.

4. In the house to the left of the Horse Guy's arena. Climb all the way up (above Tengu), there is a chest in the attic.

5. The blazing bull right before Ashina castle. Not optional.

AFTER ASHINA BURNS

6. Fat Guy, where second General dude was.

Ashina Castle:

7. Third General Guy, up the stairs from the Ashina Castle bonfire.

8. Spear General Guy, in front of the building where you meet Kuro for the first time. (Ashina Reservoir)

9. Lone Shadow 1, in the hole where the game began (Ashina Reservoir)

10. Blue Samurai dude in main building. Grapple around the building, first right then left side around to get to the window.

11. Purchasable from merchant at dungeon entrance, across a bridge from Ashina Castle Bonfire.

12.

There's a secret room in Ashina castle a bit past the Antechamber idol. In the room with the two blue-clad samurai that has the hole in the roof, there's a painting between two sets of armour, wall-hug to go in.

AFTER OWL INVADES ASHINA

13. Lone Shadow 2, at the Great Serpent Shrine bonfire, where it goes to the Sunken Valley.

14. Second ogre, bottom of main building below blue samurai dudes. You can jump down between the paths they patrole.

15. Lone Shadow 3, where blue samurai boss fight was

AFTER ASHINA BURNS

16. Spear General Guy Round 2. Right at the Ashina Reservoir bonfire.

17. Below Isshin's Hideout, blue Samurai Guy with red eyes.

Hirata Estate:

18. Spear Guy in Hirata, before Bamboo Slope bonfire.

19. Juzuo (drunk guy in Hirata), before Butterfly Lady.

20. Behind shinobi wall in Hirata Estate, in the building between Juzuo and Butterfly.

SECOND HIRATA MEMORY, requirement for Purification Ending, but can still do other endings after getting those two

21. Lone Shadow 2: Poisonous Boogaloo - the same place Owl was before

22. Juzuo 2.0, at the same place he was before

Mt. Kongo:

23. Giraffe Centipede Thing, in the huge building on the right side after Temple Grounds bonfire.

24. Dive in the pond after Temple Grounds bonfire.

25. Armored Warrior, right before Temple Grounds bonfire.

Sunken Valley:

26. Snake Eyes Shirafuji (where the snipers shoot you)

27. Long-arm Centipede Giraffe (after Gun Fort bonfire)

28. Cave after Gun Fort Centipede Giraffe, entrance is below floor boards in boss room.

29. Hidden area with mini-pyramids before Gun Fort. Go back from the under shrine bonfire, where the two dudes are. Follow that way, you jump down to it.

Ashina Depths:

30. Snake Eyes gal, at Poison Lake with statues.

31. On top of statue in Poison Lake (with Snake-Eyes) - before the bigly big room after Snake Eyes, grapple left, duck under and jump up.

32. Double ape fight, unlocked after beating Guardian Ape in the Sunken Valley

33. Double ape fight, unlocked after beating Guardian Ape in the Sunken Valley

34. Drunk Guy in Hidden Forest, before Fog making music playing boss thingy.

35. Chest in Mibu Village Lake

36. O'Rin of the Water, after the Water mill Bonfire

37. Mibu Village above water wanting guy on altar, after O'Rin

Fountainhead Palace:

38. Second bull in water palace, left side of the garden with the many soul sucking things, go there from bonfire at the broken bridge

39. Bottom of Giant Carp Lake

40. Okami leader, lightning dude on tree

If you spot any mistakes, let me know!

^{Oh my gosh, thanks for the award!!}