I tend to take contemporanous notes from many regular meetings (i.e. my personal minutes of meetings), and I also like a program I can drop various pdfs and documents onto and easily catalogue them for later reference. I've worked through most of the mac notes-taking programs. I used to use DevonThink Pro Office, and there wasn't much wrong with it, though the versions aren't particularly pretty in terms of design. Yojimbo also worked well. In the end, though, I've settled with EagleFiler. It archives emails easily, handles multiple libraries well, you can store private libraries in encrypted disk images (e.g. managed via Knox, or EagleFiler can do this itself). The encrypted library feature is the thing I that really sold EagleFiler to me. In the end, DevonThink and Yojimbo aren't bad programs, but having multiple libraries, including some kept privately, has been very handy.
I'd love it if it sync'd easily to the iPhone, but at least there are good instructions for getting files from EagleFiler to the iPhone via Airsharing or equivalent. Sadly no syncing, at least not yet.
Anyway: EagleFiler is robust, reliable, well-developed and with a responsive developer, can work with encryption and multiple libraries, searches quickly, and is easy to use. I can't see me changing anytime soon.