I currently use Evernote but also use DevonThinkPro for organizing all the documents I scan. DT has a note taking capability but it sucks compared to Evernote. That's the irony these days, you can't find a solution that lets you bring all the things you do together....doc capture & scan, note taking, bookmarking, story clipping and maybe even throw in a little project management since many times the reason you are doing all of this stuff is centered around a topic or project you are working on