This past month I switched from Endnote to the reference manager Papers. Papers unlike Endnote X6 syncs your pdf library with your iPad or iPhone. And Papers is a lot cheaper than endnote. I have also enjoyed the search capabilities of Papers over endnote, and Papers does a better job of importing PDFs and finding the citation information automatically. Papers also allows for in-text citations, and you can insert citations while working within any program.
I have also been using Scrievner for the past year, which is a word processing program built for how you actually write. It is constructed on the philosophy of working on sections of a paper rather than the whole paper. You simply create sections, and then can reorganize the sections at a later date. It is both writing, organizing, and outlining at the same time. It also has a nice project goal feature that monitors the writers’ number of words at each writing session until the project is complete.
Both programs work on a Mac or PC and were created by independent developers. Papers was recently purchased by Springer publishing, and I assume Papers will be an important competitor to Endnote in the future.