Robert at Student Tablet PC provides a nice summary of how he sets up an electronic filing system to deal with his course notes. Robert points out that while his example uses the GoBinder software program, the same effect can be achieved with other programs, as Damon shows in a detailed comment to Robert's post. Both file via the course (Robert by its number, Damon by its name) and have sub-areas (Robert divides by lecture date and also by other types of material such as Essays). Damon uses a combination of Outlook and OneNote to handle his notes.
While both Robert and Damon use tablet PCs to write and file their notes, their general strategies can be adapted by students who use regular laptops or even desktop machines. In these cases, the student might either scan the lecture notes or just keep them as paper, but the filing strategy could be used for keeping track of other materials related to the course, such as the images being studied.
Robert will be doing a follow-up that deals specifically with note-taking.