Currently using Zotero to pull biblio information from journals/the web, but then storing that information along with .pdfs/notes/qotations in its own folder in Devonthink Pro. I always have a separate window for writing notes and relevant quotations that saves along with the .pdf that I'm simultaneously annotating/high-lighting. At the top of the notes page I paste (from Zotero) the bibliography information in my discipline's most commonly used style. I like to keep everything in Devonthink so that I can easily organize current projects, "to read" lists, themes and topics, etc. Many folders and subfolders and sub-sub-
For writing, I like to start in scrivener, but format and "craft" in Word. Zotero also works smoothly with Word, by direclty importaing citations and bibliographic information for a works cited, but at the moment, my Zotero files are very unorganized, so I have that gargantuan task ahead of me...
I've heard great things about Sente's annotation system, though, so I may check that out over the summer.