Forum member jay did a video with AE-animated horse legs awhile back, you should ask him about it.

What jay wrote to me just incase anyone else wants to know how to do this......

It's true that I did animate a LEGO horse's legs once using After Effects. The short story is that it isn't easy and that the method I used is extremely limited - it only works directly side-on and under basic lighting conditions.
What I did was to take a still of the horse and divide it up into overlapping layers - the neck & head, tail, saddle, torso, upper front leg, lower front leg, upper back leg, lower back leg and then duplicates of the legs for the far side of the horse. Then in After Effects I set all layers to pivot at the proper point and the parent/child relationships (lower leg is a child of upper leg which is a child of the torso, for example) to essentially build a 2D puppet in AE. That was in AE 6.5, the newer versions have a puppet tool that might work even better.
The real trick is getting these new moving parts to move without revealing that they are stills - highlights don't move and by default they don't cast shifting shadows as they move. I used a lot of drop shadows and masking to simulate these effects.