Shelfster is a free site that allows you to bookmark and annotate websites while researching. You can create a document, edit it with a simple drag/drop of links, or type in your document as well. Then save it online (as part of the free account you create) or download it as a PDF.
Shelfster also has an iPad and iPhone app.
Shelster can help students organize their internet research. Shelfster will soon integrate with Google Docs, which could allow students to share and peer edit their research.