BibDesk 1.3 was just released (see here for very complete release notes), and this release adds a few features that were requested four years ago - searching PubMed and libraries with Z39.50 support. If you use those resources, this means no more downloading files to import references - just search from within BibDesk, and your results show up as a group that you can browse and through with the same interface you use for your local references.
Other notable features include using URLs or scripts as sources for external groups - if you have a script that can generate data BibDesk can read, its output can show up as a group.
Two new data formats are now supported for importing - MARC (and some MARC XML) and Refer. Dublin Core XML is also supported.
Note that this is also the first version that will no longer launch on Mac OS X 10.3.9.
Kudos to everyone involved - check out the contributors wiki page for who to thank!