[UPDATE: Dan Gies has provided a free puppet rig for download, with versions for both FreeForm Pro and FreeForm V2.]
Daniel Gies has created a deep and detailed series of videos about rigging and animating a character in After Effects.
Here’s a 5-minute overview of the series:
This series is for intermediate and advanced users of After Effects; it moves rather quickly and assumes that the viewer already knows the basics of how to work with layers, properties, effects, and expressions. (If you don’t, then start here.) Also, the series does not walk the user through a set of steps to create a specific result; rather, it teaches principles and techniques that experienced users will be able to adapt and make use of in their own work.
The series is broken up into pieces that are between 5 and 20 minutes, with the whole being around three hours. Here’s a link to part 1 on the AETUTS+ website, where you can also find links to the other parts.
Rich Young has mentioned Daniel’s series a couple of times already in his articles, including in this excellent roundup of character animation resources.