Academic Work Flow: How do you organise your PhD using software?

I'd love to hear how some PhDs manage their research and writing processes using note-taking, database and bibliographic software.

I'm having trouble wading through all the many options available. I'm in the humanities and know I want to use Scrivener for drafting (because I already own it), but I'm wondering what other software might help. I'm not a complete luddite, but I don't love faffing about with tech either. I need a process that's so EASY, it becomes second-nature, otherwise I'll fail to keep up with it.

I can't seem to work out if there's a program that does all three of these things: organises large amounts of research in endless formats (PDF, webpages, images) easily; enables extensive annotation of PDFs; generates bibliographic references for the research collected.

If there isn't, why the hell not?! :wink: