Contraptor modeling is primarily done in Google Sketchup. Sketchup is free, very easy to use for both novice and pro, and extensible with scripts and plugins (we wish it was open source, too). While you can use other 3D modeling apps, there is already a large library of "official" Contraptor components available on Google 3D Warehouse for download directly to Sketchup and building your projects.
If you've never used Sketchup, you can get started after watching a couple of tutorials here: http://sketchup.google.com/training/videos.html
The following tutorials demonstrate basics of importing and working with Contraptor components in Sketchup: