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Getting back to the topic of research-heavy writing (which I do a lot of for the various assignments on my Egyptology degree), I just use plain old Word. As I'm researching the subject I'm creating my bibliography, and making notes on each source, with each source starting a new page. When I start doing my actual writing, I start it at the top of the same Word file, and as I use each note I've made, I change its colour to red, so I can easily see what I've used, and what I haven't. At the end, I delete all the notes (keeping them in a separate file, of course) leaving just my bibliography at the end of the file. Works well for me.
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