Jonathan, I separate the wealth of research I do from the "jamming-photos-and-text-and-pdf’s-into Scrivener," which I do as well.

I've been using MacJournal, but David's post made me ding/think back at my shock at revisiting NoteTaker as few weeks ago. I realize, as a result of reading David's post, that can do one book diary with the research stuffed into each chapter...really easy to do with its section tabs.

I am also partial to pretty tools. I like the tools I use to look good. So shoot me, I like colors.

I like MacJournal, but if I relearn NoteTaker (and there is a learning curve for efficient use) it is going to be a lot better. You can export to RTFD (with attachments) or print to PDF, which for me is useful to have beside my computer when working on chapters because I am sloppy about recording attribution, I'm writing non-fiction these days, and I absolutely cannot risk one word of plagiarism.