1. I use Devonthink Pro for notes / research: http://www.stevenberlinjohnson.com/movabletype/archives/0002....
2. Many use Scrivener for writing, but I have never quite managed to agree with it properly, so I just use Word.
3. I use Bookends: http://sonnysoftware.com/ for citations. No one it seems really likes their citation manager, but I like this one best.
See also http://blogs.plos.org/neurotribes/2011/06/02/practical-tips-....