The Most Important C&M Links:
It seems only fair that I link to the webcomic which first inspired me to do this in the first place... but unfortunately, the original site is no longer online. The world has become that bit less bright a place for its absence.
It may not be the most sophisticated of animation programs, but Anim8or offers a great introduction to 3-D modelling and animation, and has made itself very useful in my workflow for doing stuff like C&M. As stated under #1 in the Series 1 Production Notes, most of the characters (except Blue Thing) are rendered from 3-D models in Anim8or, as are the more developed sets such as the Peruvian sewer... Try it yourself. You never know, you could end up writing a really appalling webcomic like mine...
The GNU Image Manipulation Program
I've been using the GIMP (as it's known for short) for all sorts of projects for several years now, and as of Series 4 it's also found its way into the C&M workflow. Highly recommended for all your image-editing needs.