Yes, in fact there are:

RefWorks, which also has a tool for embedding your citations in your proper format into a Word document, and is supported by countless academic electronic references (see that export to RefWorks button in FirstSearch and PsychInfo, f’rinstance?).

The open source WikiNDX may also suit some folks’ needs, having some interesting note-taking and aggregating capabilities.

It’s all about what tools work for you.

also, as atom probe suggests, there are two forms of on-line reference managers both using centralized server solutions. The first, citeulike etc. you have little control over and, as you say, do indeed run the risk of becoming trapped. The second, the server and its all important data is in your hands (or your institutional technical support if a shared resource) and these are applications like refbase and WIKINDX.

re. the use of plug-ins for importing/accessing bibliographic data into external ‘productivity’ software (presumably word processors), why not go for an all-in-one solution such as WIKINDX (my program)? Rather than messing about with plug-ins, compatibility issues etc., WIKINDX integrates a WYSIWYG word processor capable of Rich Text Format output in which references and quotes, paraphrases etc. can be inserted direct from the database (no more re-typing of long quotes). Bibliographies are automatically generated and citations automatically formatted (footnote, endnote or in-text styles — including context-sensitive citation formatting).

I agree that hosting your own reference manager is — as a general rule — the best way to keep you hands on your data. But for users who (1) don’t have the technical skills to do this or (2) don’t have access to a server or (3) just don’t want to bother with software installation, both CiteULike and Connotea are excellent solutions. I confirm that both allow exporting the full library or a subset of your references in multiple formats.

If you aren’t hosting your own reference manager, you should definitely check how good the export of information is: most of the webapps have Endnote and/or BibTeX export, but some don’t export all data!

the way I see it, syncing and importing/exporting really are two different things. You don’t want to overwrite your whole local reference library anytime you have a new item in your online library. As a registered user you can dump your whole CiteULike library in Endnote format. Most reference managers allow you to import/export to/from Endnote (as well as many other formats). But dumping a library is more useful for security backups than for updates, that’s why I still look forward to real synchronization support. My 2 cents…

If there are, please name’em!