Zotero – Mendeley – BibSonomy
Well, I prefer Zotero because it is a universal tool for importing bibliographical data from any kind of source that supports a Zotero importer. You keep your bookmarks right in your favourite web browser and export them to your favourite text editor for further processing there. Synching with a web server is an option, not a must. If you work with BibTeX, as I do, an alternative to Zotero could be BibSonomy which has excellent BibTeX import and export too. Mendeley also supports the latter, while Mendeley’s main strength seems to me automatically extracting the metadata from PDF files for building your bibliography file in the first place. What all those platforms have in common are certain social web features such as connecting to friends, subscribing to groups or bibliographies of other users etc. This might of course be of some interest, but it’s certainly not at the centre of bookmarking and managing your bibliography. If you are looking for a web 2.0 platform for scientists you might like to have a look at the comparison in German-language IT magazine c’t 25/2009, pp. 78ff.