If del.icio.us matriculated

Citeulike lets you store bookmarks to papers indexed by several resources*. The bookmarklet is really smart — parsing the paper’s title and authors from an index’s citation. Additionally, it automatically links the authors’ names so you can browse other papers they’ve written (although without authority control this is less useful with more common names). I think all users can add notes to any paper as well (haven’t explored it that far). Like del.icio.us, it has a shared tagging system.

*Right now that includes PubMed, JSTOR, ACM, arxiv, and CiteSeer (thanks for adding that last one, Richard).