Richard Cameron (I think) has cooked up a del.icio.us like system called CiteULike that has a vertical focus: academic papers from the sciences (biology, medicine, computing). Need to kick the tires on this one, but I wonder if it restricts URLs to the listed academic paper sources?
This led me to another whacky idea regarding metadata gathering in a social bookmark service. del.icio.us doesn't do anything special with your bookmarks, while services like Furl.net claim to archive entire documents. In between, those two points a service could analyze the documents, they're probably in PDF or Word, gather empirical observations about documents, users, and tags, and display that to users for browsing and navigation. For example, start doing the CiteSeer thing and mining bibliographies, but now you have all this other social translucence data. If you limit the domain of documents referred to, then you can probably start to make some interesting inferences about relevance and importance.
CiteULike would be a nice service to tie together with Google Scholar