Google Notebook (http://www.google.com/notebook) is a great tool to use help you keep track of notes and links. You can organize your links by topics and you can install the Notebook in your web browser. So when you need it, it accessible.
I really like the Yahoo Search Pad tool (http://tools.search.yahoo.com/SearchPad/Video.html). While you are searching Yahoo is paying attention to your search and after a few messages Yahoo asks you if you want to record and save your search topics. You can save your search topics and links and organize them. It's really a great feature to help you keep track of topics when you are writing a paper.
There are other tools that do similar things as the two listed above. Some may even be better. Just remember, with all these tools, don't copy someone else's work. Yes, take notes, but write your own paper!