I just came across an article on GaveDev Tuts+ called 16 Tips, Tools and Resources for Your Next Game Jam. Great info in the article. Lots of good articles linked, but also lots of good resources linked. I found a number of free tools linked that we actually were using when we did the Indie Speed Run last month. For example, Bfxr for sound effects, Tiled for map editing, and Aseprite for sprite editing.
I really should do a post about our experience doing the Indie Speed Run. It was an intense, but extremely valuable experience.