Currently, I'm writing a paper in Microsoft Word 2007. I use Endnote to organise my references and bibliography and hold electronic copies of papers I've found where possible. I have stacks of books by my desk and a fairly disorganised (physical) folder of papers. I currently use Diigo (in conjunction with the bookmarklet for Chrome) to store, highlight, annotate and tag online articles of interest.
I am partly interested to know if there is a system out there that combines all these things but I'm guessing that's more of a question for the SuperUser Exchange. Ideally, I would like to write in a tool like Google Docs/Drive so that I have a revision history of what I've written but I think I will have to move everything to Microsoft Word for submission eventually anyway.
What I really want to know is if there exists a productivity method for rationalising the bookmarking and citation side of things. I've heard Zotero and Mendeley are both services to explore and I've started using Evernote to store ideas on the go but without some kind of framework I fear I'm at a loss as to decide which tool is the best fit. I'm interested generally in what services people use for recording ideas (their own or others') when writing or doing research, how they find these affect their productivity, and how they link these services up with a method to facilitate a better articulation and presentation of ideas. As someone fairly new to the idea of productivity methods, do they affect which tools one decides to use?
If anyone knows of a way to link up the services I have or move easily to a more efficient system, I'd welcome those kinds of suggestions too.