As cloud based computing becomes increasingly common, more and more note taking programs will allow you to save your notes to the cloud, so that you do not run the risk of losing them in case your computer crashes. Google docs is an obvious choice, but listed below are some of my other favorites. (With thanks to The Pursuit of Technology Integration Happiness).
Evernote: This is my absolute favorite note taking program. In addition to regular note taking, Evernote also allows you to save and organize content from the Internet as well. If you have not already, try this program!
Penzu: More of a journal form, but still a good way of taking and organizing your notes.
Simplenote: Very simple note taking program, and you can easily share your notes as well.
Workflowy: Allows you to create notes in an outline format. Very easy to use.