Mahou no Hiroba

https://en.wikipedia.org/wiki/Clay_animation

Includes clay, gypsum, and plasticine animation.

Part 1: https://myanimelist.net/stacks/30395
Part 3: https://myanimelist.net/stacks/50904

Music videos using stop-motion animation.

Part 2: https://myanimelist.net/stacks/43980
Part 3: https://myanimelist.net/stacks/51619/

Removed after creating this list, since I'm not sure if stop-motion was used, but it's still a nice puppet clip:

https://myanimelist.net/anime/42853/Kotobadori

These stacks are meant for cataloguing every stop-motion animation on Myanimelist. The list is the result of research by the Stop-Motion Animation Appreciation Society:

https://myanimelist.net/clubs.php?cid=16200

Stop-motion is a form of animation in which objects are manipulated little by little while each frame is shot separately. Puppet animation is the most common, but before 1935 cutout animation was also very common. Among other types are claymation, pixilation (now removed from the database), object and model animation. In this list also works using sand, charcoal or paint are included, since in the form they've been accepted to MAL, they also include gradual manipulation and shot by shot filming.

Part 1: https://myanimelist.net/stacks/47018
Part 2: https://myanimelist.net/stacks/47020
Part 3: https://myanimelist.net/stacks/47021
Part 4: https://myanimelist.net/stacks/47022
Part 5: https://myanimelist.net/stacks/47023
Part 6: https://myanimelist.net/stacks/47026

Part 8: https://myanimelist.net/stacks/47032
Part 9: https://myanimelist.net/stacks/47034
Part 10: https://myanimelist.net/stacks/47035
Part 11: https://myanimelist.net/stacks/47036
Part 12: https://myanimelist.net/stacks/47038
Part 13: https://myanimelist.net/stacks/49186
Part 14: https://myanimelist.net/stacks/51880