I got fed up with EndNote a few years ago, when versions 8 & 9 seemed to constantly hang and crash. Since then, I have used Bookends extensively, and now use Sente. This review is for Sente 5.7.5 (this version not yet being listed on Versiontracker).
Both Bookends and Sente are excellent programs. I have used Bookends for a couple of years, with a large reference library (>6,000 references, >1,200 downloaded pdfs), and have been impressed at wonderful support from the designer. However, the fact that Pages 09 has opened to EndNote integration made me look at all the reference managers again. Whilst I think the EndNote integration in Pages 09 is very effective, I still find the EndNote interface and user features clunky. Bookends has a straightforward interface and many lovely features for updating references, downloading and filing pdf files, and importing references from PubMed or pdfs. However, it can only scan saved Pages files. I sometimes find myself saving a Pages file, formatting it, then exporting it to Word to share with colleagues or publish, which is a drag. Sente, on the other hand, has some lovely lovely features for searching and importing references from pubmed or pre-downloaded pdfs. It's easy to use, and looks lovely. Even more handy, it can scan open Pages files, reducing somewhat the effort of formatting bibliographies. It's still not the full integration with Pages that EndNote X2 offers (how I wish Apple would open up Pages to other developers), but it is easy and helpful. In summary, if you're frustrated with EndNote, or just wish your reference manager could do more and help you handle all your pdfs more easily, then Bookends and Sente are both great programs. For Pages 09 integration, though, Sente just edges Bookends so far.