I'm seeing people mention applications they've used and recommend but the recommendations are buried deep into other threads so I thought starting a top level thread for recommendations might be useful.
I'd like to add a specific request to Christie's call for most useful no fee applications. In December Catherine Fichten and Jennison Asuncion of Adaptech.org will be joining us in SCoPE for a seminar discussion on Accessibility of eLearning. Adaptech is currently seeking information about free software that would benefit students with disabilities, so I thought we could help them out by gathering some ideas. I created a section in our Open Source and Free Software Wiki so anything posted here I'll be sure to copy to the wiki.