If you are an academic, CiteULike might be a tool you'll enjoy. CiteULike is like Del.icio.us, but oriented to academic papers. In addition to the regular bookmarking and tagging that Del.icio.us does, CiteULike allows you to enter all the relevant reference data (presumable if someone else has already done it for a URL, it will just be there for free), put in the abstract, and enter a note. You can generate EndNote and Bibtex entries for papers and even upload a private PDF of a paper. Like Del.icio.us, there's RSS for accounts.
One thing I like is the group feature. I can have all my research assistants sign up for an account and then group them together to see the collection of papers they're all referencing. Of course, you could do it for a class as well. I've had my students doing this on our lab wiki and even entertained ideas of creating wiki pages the understand Bibtex, but this beats anything I could put together on my own.