Multivalent
Have trouble keeping track of papers you print out? Can't read online copies because you need to mark them up with notes and comments? Try Multivalent, program designed to help you work with digital documents. You can annotate your PDF files, for instance.
Web Annotations
In a similar vein, there are projects to allow third party annotation of web sites. You could, for instance, read the electronic edition of the Ap J (the HTML version, not the PDF's) and use these tools to store your notes. Check out the Annotea server and the Annozilla plugin for Mozilla.
Online Books
Everyone should know about Project Gutenberg and the Online Books Page.