I found Scrivener extremely useful for my own doctoral work. It allows you to move content easily between chapters without having to have multiple documents open. You can keep notes directly in the program. It also lets you set a target word count each day, which helps maintain the discipline required to finished a dissertation. A bit of forewarning, the program differs a bit between PC and Mac. I preferred the Mac version and found it easier to use.

You'll also want some kind of software for citations management and formatting bibliographic data. There are many options to choose from, Refworks, Endnote, and Mendeley being examples. The one I use is Zotero, which is open source, free, and receives regularly updates. It integrates well with most web browsers, so saving citations is often as easy as clicking a button when you have an article open from a database like JSTOR.

Zotero has plugins that integrate it with Google Docs and Microsoft Word, and it can automatically format footnotes and bibliographies in these programs. Unfortunately there is no simple way to integrate Zotero with Scrivener. You can manually drag citations into Scrivener from Zotero, but they won't format automatically or easily let you create a bibliography. I simply imported my final dissertation draft into Word and manually replaced the footnotes, which was time consuming but not too difficult. Despite the difficulties of getting them to work together I found both programs essential to my writing.

One thing I really wanted when I was writing my dissertation was a good way to organize and view photos I'd taken in the archives. I'd especially wanted to be able to add notes and metadata to photo files. Since I started my doctoral work, Trophy was released, and promises to do this. It's free and open source. I don't have much experience with it yet, but it looks like a great research tool.

Hope some of that is helpful. It would be good if academics talked more often about what tools they use and how to optimize workflow.