I am in the process of finishing up a Motion Graphics I (After Effects) class and my final project is due this Monday. Here is an earlier project that I did -
YouTube - Thunder Over Michigan 2011
I would suggest the book "Creating Motion Graphics with After Effects" by Trish & Chris Meyer a good place to start. I also find knowing how to use Photoshop and Illustrator will be beneficial in learning After Effects.
The last project is what you are talking about, it gets into using the Puppet Tool, using Particle Generators, etc...