Short answer: Blender.

Long answer:
1) I get ideas, and a random one gets me motivated.
2) I think about it for a while, let it ferment a bit. (Definitely not procrastination)
3) I do the basis of the scene with cubes and planes, import the models and put them in their pose in the first frame.
4) I animate the Torso and the neck, then the legs and arms, then the face, then go back to make sure it all matches the face.
5) I set up the lightning and fine tune the camera motion if there is any
6) MMD physics don't work in blender, so I use the wiggle bones addon to fake the physics and bake their animation to another layer.
7) Rendering. Takes a day or two.
8) I import it to blender video editor and add any effects or sound I want to, then export as mp4

yeah