Have you discovered Zotero, yet? It's billed as a "personal research assistant," created by the folks at George Mason University and funded by both the Andrew Mellon Foundation and the U.S. Institute of Museum and Library Services. And it's free.
A Foxfire add-on, Zotero helps researchers gather and organize resources, take notes, cite sources in more styles than I've even heard of, create bibliographies and share results. Students can save websites, highlight add sticky notes, created note cards--it's great! It even works with many databases, such as JSTOR.
I was thinking of subscribing to NoodleTools for the school next year and using it with Diigo, until one of our tech guys sent me the Zotero link. Now, I plan to make Zotero's installation and basic training part of Day One for all research projects.
The Zotero site also includes several good tutorials on both a basic and advanced level.
Definitely worth checking out!