This is a guide on how to find all (or at least most) of the skeletons in the game. If you're anything like me, you'll want to raise a lot of them. Gotta dig 'em all. Use the following map as a visual aid.

I counted 23 skeletons in the game (that I found after 2 playthroughs, if you found more, post 'em in the comments). The very first skeleton you use Animate on is guaranteed to leave your employ and go on an adventure of a lifetime, so you'll only be able to have 22 at most.

2: need to be dug up; make sure you have defensive rituals up because some townsfolk can wander even at night

The ones where you could find Nightshade for the Torpor recipe.
2: need to be dug up

3: need to be dug up (don't dig up graves right in front of the graveyard fence, they're empty and you're guaranteed to get caught)

1: in a sarcophagus near the entrance

1: in a sarcophagus near the entrance
1: follow the left wall, after 2 gul encounters, in a sarcophagus
1: follow the right wall, after 1 gul encounter, in a coffin
2: through the tunnel in the north-western corner of the entrance chamber, after 1 gul encounter, in a coffin and a sarcophagus

3: need to be dug up

1: in the tunnels; need to succeed on investigation 4 check followed by strength 3 (or you could make Boerhaven's creature open the way with no check)

You'll have to win at least 2 combat encounters to get them.
1: second level, right after clearing the first room of patchas, sitting near a gibbet
1: second level, in the room where the Hammerling lived
1: second level, after the Hammerling fight, follow the right wall, on the floor in the room with 3 floating blue orbs
1: second level, after the Hammerling fight, follow the left wall, behind a secret door (need to succeed on analyse 3 and investigation 5 checks), sitting on the throne; this skeleton has slightly higher base stats

1: sitting at a tree trunk near giant webs

Right in front of giant webs; slightly back away from the big cave entrance and you'll see a small one to the left.
1: follow the left wall, near the scroll of Animate+ (there will be no scroll if you found it in the dungeon already)