Since the start of Nepomuk I've been using bibsonomy for bookmarking and keeping track of citations (My bibsonomy page). It's not quite as slick as del.icio.us, and since the user-base is only a fraction of del.icio.us' the social aspects are probably not as good, but I never found the social bit particularly useful anyway, and the bibtex/citation thing is very cool.
(re: the social aspects, it reminds me of something I read pointing out that all the cool tag-cloud, tag-clustering, folksonomy things from del.icio.us, flickr, etc. are not the main purpose of the site, and also not why people using them. People come to keep track of their own links/photos/movies/whatever, and the folksonomies is just a side-effect of this. I would put a link here if I remembered where :)
… Anyway, bibsonomy is nice, but it quickly becomes like a black hole where links go in and never come out. Trying to fix this is of course the bibsonomy tagging extractor in gnowsis (yes,we do del.icio.us and flickr as well), but that's just moving it to another black hole. There is a RSS feed from bibsonomy of course, but I'm not sure what to do with it. Other feeds I follow are converted to email with rss2email, but that's not what I want here. The RSS integration in firefox sucks beyond measure:
well, the links are there, but it's hard to scroll, and no way to filter/search. SO (slowly, slowly to the point), I write my own, modelled slightly after the python sidebar. Here, in all its glory:
It auto-searches as your type and is slightly better than going to the bibsonomy web-site itself, but only slightly. What I really would have liked was way to integrate bibsonomy with quicksilver (like you can with del.icio.us, oh the pains of supporting your fellow researchers), but diving into object-c and xcode to write a new plugin seemed too complicated.
Anyway, there is still a slight problem with the sidebar, searching is only done on the description and title, not the tags… this must almost be a bibsonomy bug though, so i'll whine on the mailinglist.
Finally, should you for some reason want this wonderful sidebar for yourself, click here.