EndNote was the top tool for reference managing, but the earlier versions went through a phase of frequent crashing, and I went off and tried Bookends and Sente instead. I came back to see what EndNote was like, since it offers tight integration with Pages and Word.
The direct integration with Pages is a big plus of X2. However, Sente, and now Bookends as well, will scan open Pages files. Sente and Bookends are both streets ahead in terms of mac-ness; Sente is particularly lovely. Both Sente and Bookends have a host of great features for filing and handling pdfs. In the end, Sente allows me to scan open files in Pages or Word, handles large libraries reliably, doesn't crash, is very pleasing to look at, allows me to easily access linked pdfs, and is very good at importing new refs into the library (e.g. when you drop a pdf on the library). EndNote has become much more reliable recently, but it's still less flexible and less pretty than Sente. Both Sente and Bookends have similar feature sets and are excellent programs.