This one can be kinda hard to get, since they're on almost every scene of the game. Here are their locations, courtesy of the Metal Gear Wikia page:
1. Dremuchij South: From the ledge overlooking the tree where your backpack was hanging, look south with R1 to see it sitting on the edge of the hill. You can also use R1 to spot it by looking up and to the east from southwest of the tree, although it's a harder target to hit from here.
2. Dremuchij Swampland: On the "wall" to the southeast of the fruit tree past the swamp.
3. Dremuchij North: On top of a hollowed-out tree stump in the easternmost part of the large clearing to the northeast.
4. Dolinovodno: On top of the pole, connecting to the Bridge closest to you to the left.
5. Rassvet: Through a hole in the west side of the north wall of the factory, near the stairs, look through the hole to see the Kerotan.
Operation Snake Eater
6. Dremuchij East: Under the logs on the western side of the northern clearing. Use R1 to look down at it from the north. Note: You will not be able to return here after you drop down into Dremuchij North. Shortly after that, you'll lose your M1911A1 until you meet up with EVA in Rassvet. If you don't have the Patriot, the Single Action Army, or the EZ Gun, you'll either have to double back to get the other Dremuchij and Dolinovodno kerotans after you get the AK-47 from Rassvet before you trigger the Ocelot Unit fight there, or you'll have to collect grenades and learn how to throw them very accurately in order to hit the kerotans. I recommend waiting, unless you're really confident in your ability to land grenades on small ledges.
7. Dremuchij North: On a ledge near the middle of the northern half of the map. Climb the one climbable tree and look to the west. Alternately, stand on the northern edge of the patch of grass with birds in it under the golova tree, and look up to the northeast.
8. Dremuchij Swampland: On the northwestern bank of the swamp, behind the cluster of trees on the northern part of the bank. It looks like it's close enough that you could kick it, but it's not.
9. Dremuchij South: In the area to the southwest that's blocked off by a fallen log, on a ledge on the northwestern "wall". Note: You will have to crawl under the log that you crawled under to get your backpack.
10. Dolinovodno: In the original NTSC releases (Japan and North America), it's where it was in the Virtuous Mission, but on the north of the bridge instead of the south. In later releases (the PAL/European release, Metal Gear Solid 3: Subsistence, as well as the Metal Gear Solid HD Collection), it's on the "wall" to the east of the northern side of the rope bridge.
11. Rassvet: Under the stairs. Use R1 to look under the stairs from the east. You might need to wait until after you meet EVA and fight the Ocelot Unit.
12. Chyornyj Prud: Underwater next to a tree between the northeastern exit from the area and the ledge holding the Crocodile Cap. Either throw a grenade at the base of the tree from the shore, or just shoot it while diving underwater. Note: The GA-KO camo is in this area, in the water to the southeast of the northeastern exit. Watch out for the nearby gavial.
13. Bolshaya Past South: At the base of several trees immediately next to the eastern portion of the northernmost electric fence.
14. Bolshaya Past Base: Under the table in the bedroom in the main building. Note: Before leaving this area, make sure that you have all kerotans and other items up to this point; you won't be coming back.
15. Bolshaya Past Crevice: On a ledge to the southeast. You might want to use R1 to look for it while Ocelot is reloading. You'll only be able to hit this kerotan during the fight with Ocelot; once he's beaten, you leave the area automatically.
16. Chyornaya Peschera Branch: In the hidden room with the Night Vision Goggles. To get there, go northeast from your starting location into the next part of the cave, go northwest to enter the flooded cave with the waterfall, enter the branch that leads northwest, avoid falling off of the (admittedly short) cliff here, crawl through the small cave to the northeast, crawl through another crawlspace directly in front of you leading to the southeast, then follow the passage into the cave with the kerotan and the Night Vision Googles. Watch out for the pit between you and your quarry. If you can't see the frog, it's on the wall on the far side of the pit (that is, the south side); you might need to pick up and equip the NVG, light the Torch, or throw down one or more Russian glowcap mushrooms in order to see where it is. Once you have the Night Vision Googles and the kerotan, it's much quicker to drop down the pit than to go back through the crawlspaces.
17. Chyornaya Peschera Cave: In the hole in the cave ceiling over where The Pain appears. You can see it from where you start the fight, or from The Pain's platform once he's beaten; hitting it from the shore before the fight is possible, but difficult, and you'll need to use the Directional Mic to make sure that you did actually hit it. Note: Once you slide down the incline at the start of the next area, you won't be able to come back to either of the first two Chyornaya Peschera areas. Also after defeating the boss you can pick up the Snow suit.
18. Chyornaya Peschera Entrance: On a ledge overlooking the alcove with the Claymore mines in the middle of the area. If you shoot the claymores, the explosion might hit the kerotan, but it's not guaranteed. Alternately, pick up the claymores by crawling over them, then shoot the frog from between where the mines were placed.
19. Ponizovje South: On the shore to the northwest of where you enter the area. Move forward a few feet and you should be able to spot it.
20. Ponizovje West: Underwater, in the large grate on the north wall. You'll probably need to get in the water to shoot it.
21. Ponizovje Warehouse: Exterior: On the post on the gate to the west of your starting position.
22. Ponizovje Warehouse: On the concrete ceiling rafters on the side where the exit is, but it's not visible from the upper floors. While on the bottom floor, aim up and shoot it from the far hall that leads to the red hinged doors.
23. Graniny Gorki South: On a tree branch immediately southwest of the north exit. Get it before or after the fight with The Fear; it's not worth the bother during the actual fight.
24. Graniny Gorki Lab Exterior: Outside Walls: To the left of the wall. If you crawl back into this area from the Inside Walls area through the opening in the wall, you'll see the kerotan right in front of you.
25. Graniny Gorki Lab Exterior: Inside Walls: Inside the boarded-up building in the southeast. You can see it through the windows on the east and west sides of the building, although the shot is very difficult to pull off through the east window.
26. Graniny Gorki Lab 1F: On the first floor, east of the medical room with the scientist inside, on top of the row of lockers.
27. Graniny Gorki Lab B1 East: In the westernmost cell, on the table next to the cell door. You can punch this one.
28. Graniny Gorki Lab B1 West: On the table in the break room between the alarm panel and the lockers. You can punch this one, too.
29. Svyatogornyj South: After backtracking from Graniny Gorki Lab, up on the cliff wall south of the entrance from the Ponizovje Warehouse
30. Svyatogornyj West: On the hillock in the southwest, next to the fallen hollow log and the pit trap.
31. Svyatogornyj East: In the bedroom in the barracks building, near the window. You can easily shoot it through the window, and with the sniper rifle, you can even hit it from above the food store building to the west.
32. Sokrovenno South: On the ledge immediately northeast of the ammo shed. Your best angle to hit it without drawing attention to yourself is by getting close to the cliff face to the northeast of the shed. If you're trying to get the kerotans during the fight with The End, always use a suppressor unless you want him to know where you are, especially if you know that he's on the same part of the map as you - and he starts out on this part of the map on every difficulty setting.
33. Sokrovenno West: In the mouth of the cave that the stream is running into. It's on the southernmost part of the map, west of where you enter this area from Sokrovenno South.
34. Sokrovenno North: On the ground next to the base of a tree on the southern part of the map. If you follow the cliff wall between the two exits to Sokrovenno South, you'll walk right past it, the first tree you pass is where the Kerotan will be.
35. Krasnogorje Tunnel: Hidden behind one of the support pillars on the west of the lower level of the tunnel. Face away from the north wall and you'll see it. Note: Once you drop down the short cliff at the start of the next area, you won't be able to come back to any previous areas. You might want to save your game here or at the start of the next area if you think you might have missed anything.
36. Krasnogorje Mountain Base: West of the exit to the next area, looking out over the cliff. You'll need to get close to the edge to get a good shot.
37. Krasnogorje Mountainside: On top of the food supply shed. Either shoot it from near the nearby machine gun emplacement, or use a sniper rifle to shoot it from the uppermost cliff path. Blowing up the supply shed with TNT won't effect the kerotan.
38. Krasnogorje Mountaintop: On the cliff wall in the far southeast. Shoot it from the south side of the southeasternmost building.
39. Krasnogorje Mountaintop: Behind Ruins: In the tall red communications tower in the Groznyj Grad facility. A sniper rifle is all but necessary to hit it.( base of the closest tower to you fron the cliff top)
40. Krasnogorje Mountaintop: Ruins: On the top shelf next to the door leading back to the Krasnogorje Mountaintop.
41. Groznyj Grad Underground Tunnel: On the red pipes in front of the door leading to the north. You can hit it with a sniper rifle before the fight with The Fury, or hit it with any firearm during the fight. Note: You won't be able to go back up the ladder and exit this area once you drop down the ladder and start the fight with The Fury. Once you beat him, you lose access to the main part of this area, including the kerotan, and won't be able to go back.
42. Groznyj Grad Southwest: In the door of a vehicle shed. The shed in question is the middle one in the western column of sheds.
43. Groznyj Grad Southeast: On the southeast corner of the prison building. Get up on the roof and you'll have a clear shot.
44. Groznyj Grad Northwest: Up the stairs in the fenced-in area containing the western guard tower. Getting a clear shot through the fence can be difficult; you might need to get up close to hit it. A better idea might be to use the boxes to the east of the fence. Climb on top of them and face west. You should have a clear shot at the Kerotan.
45. Groznyj Grad Northeast: On the other side of some bars in the underground ditch. There is an entrance to this ditch next to the food supply shed to the northeast, and another entrance in Groznyj Grad Southeast to the north of the prison building.
46. Groznyj Grad Torture Room: Under the desk in the guardroom.
47. Groznyj Grad Weapons Lab: East Wing: On top of the shelf in the northwest corner of the second floor. Raikov's patrol route will eventually take him through here. Note: Getting Raikov's uniform here makes getting through Groznyj Grad much easier; you might want to do so before you go after the kerotans and any other items in the area. Although Raikov's uniform will let you into the south corridor of Groznyj Grad Weapons Lab: Main Wing, the part of that area containing the kerotan will not be accessible until later in the game.
48. Groznyj Grad Weapons Lab: West Wing: On the guard tower to the south of the entrance to this area. You'll need to use a sniper rifle to hit it, meaning that you'll need to change out of Raikov's uniform and probably take out the guards first. Once you've hit the kerotan, kick any unconscious guards to wake them up; if they're dead, leave the area and return, and they'll be replaced. Note: You do not have to get this Kerotan on your first trip to Groznyj Grad. You can get it on your second trip back, if you happened to miss it. Simply get inside the facility and equip your scientist uniform. Run up into the locker room, where you hide Raikov, and progress to the hallway right before the sequence where Snake got caught by Volgin. Pull out your SVD and the Kerotan will be on a light post outside. Shoot it through the window.
49. Tikhogornyj: Immediately in front of the dam to the south. If you don't have the ammo to shoot it or blow it up, you'll need to double back and hit it after you've picked up your Equipment with EVA in the next area behind the waterfall.
50. Tikhogornyj: Behind Waterfall: On the pipe to the southwest of the ladder leading back into Groznyj Grad. Note: You won't be able to return to Tikhogornyj once you climb the ladder.
51. Groznyj Grad: Shagohod Hangar: Behind a pipe between two mainframes on the west side of the Shagohod, opposite one of the fuel tanks. Note: After planting the fourth C3 charge, you'll automatically leave this area, and will not be able to return to this or any previous areas, so make sure that you've picked up everything that you need in Groznyj Grad. In addition, all subsequent areas are one-time areas; after this, there is no going back.
52. Groznyj Grad: During The Fight Against Volgin: On the southwest rim of the pit. Make sure to shoot it before Volgin is defeated. Be aware that Volgin's electric bolts can and will home in on you as long as you have any metallic weapon equipped, such as a firearm or grenade.
53. Groznyj Grad (Bike Chase Part 1 - Pursued By Shagohod): On the eastern guard tower near the end, in what was once Groznyj Grad Northwest. You might be able to hit it with a sniper rifle or RPG the first time that you stop in what was Groznyj Grad Northeast, but don't bet on it. The best spot to hit it is from Groznyj Grad Northwest, where Eva will stop (the area where Snake climbs from out of the sewer after meeting Eva behind the waterfall).
54. Groznyj Grad (Bike Chase Part 2 - After Encounter With Ocelot): The Kerotan will be on the seat of a forklift, to your left, when facing the soldiers. When EVA stops the bike, you'll have a clear shot at it with R1. You might need a sniper rifle to hit it. When EVA stops the bike in this part of the chase, shooting all (or most) of the incoming soldiers will usually prompt EVA to get moving again, so don't do this if you don't want her to drive away just yet.
55. Groznyj Grad Runway (Bike Chase Part 3 - Motorcycles): The Kerotan will be on top of a sign on the western side of the runway, about halfway through this section. No, you can't make EVA stop or slow down. Good luck. Eva will be swerving all over the runway. It's probably going to take you at least a few tries to get this, so make sure you save right after entering Runway South. There will be a moment where Eva will swerve to the left, and then slowing down to swerve back to the right. At this moment, the Kerotan will be to your left front, giving you the perfect opportunity. I found this to be the easiest attempt, with an RPG-7. I also recommend equipping your Directional Mic so you can quickly equip it and check to see if you have hit the Kerotan.
56. Groznyj Grad Runway South (Bike Chase Part 4 - Shagohod Attacks): The Kerotan is on top of another sign, this one to the east near the beginning of the area, while the bikes are still chasing you. This one is much easier to hit, since it's closer to the road and EVA isn't weaving around as much. Pull out your SVD right away, and line up a shot. Try to hit it as fast as possible, Eva will be going deceivingly fast and it is easy to miss the shot if not quick enough.
57. Groznyj Grad Rail Bridge (C3 Sniping): On a closer part of the bridge's lower support structure. Stand up and pan down and to the left to see it. Make sure that you still have the time and ammo to hit however many C3 charges EVA has planted. (Directional Mic recommended).
58. Groznyj Grad Rail Bridge (Shagohod Battle): On the nearest corner of the roof of the nearby building. It's best to hit it with a sniper rifle once you're on foot, but masochists may want to do things differently.
59. Groznyj Grad Rail Bridge North (Bike Chase Resumes - Motorcycles and Guards) Between two barricades in front of the parked vehicle near the very end of this area. If you're trying to get no kills for some reason, it's easy to hit the nearest guard, as he likes to walk towards the kerotan (but won't actually walk in front of it, thankfully). The RPG-7 is best for this. (Directional Mic recommended).
60. Lazorevo South (Bike Chase - Flying Platforms Attack): On the ground to the east near the beginning of the area, at the base of a large tree stump. Use an RPG-7.
61. Lazorevo North (Bike Chase, Final Section - Motorcycles): On a rock directly in front of you and slightly to the left, near the beginning of the area. Again, use an RPG-7. (Directional Mic recommended).
62. Zaozyorje West: On a small ledge below the ravine that you cross with the log bridge. Look down from the middle of the log bridge to see it. It helps to take out or distract your pursuers beforehand.
63. Zaozyorje East: Behind a tree where the path forks to the north and east after leaving the large clearing where you enter the area.
64. Rokovoj Bereg: On top of a tree near the middle of the area. Use thermal goggles and the sniper rifle if you have trouble finding or hitting it. Make sure that The Boss isn't too close when you start looking for it; her Patriot and her CQC can and will interrupt you. Defeating The Boss starts the final sequence of cutscenes, so make sure that you've hit the kerotan before beating her.