I've looked at DT for a long time now, how does it compare to Circus Ponies Notebook?
CP Notebook is a fine tool. I have it and still use it some. Here is some info from Kerry Magruder (History of Science Dept at Univ of Oklahoma) on Mac apps for academic purposes regarding Notebook and DEVONthink. (I have a copy of this [in DT as it happens], but it seems to have disappeared from the web.):
"If your needs are simple, try Circus Ponies Notebook. Notebook is an excellent notetaking application that combines general notetaking, outlining, and project organization. I have used NoteBook for a variety of kinds of notes, particularly ones involving multimedia, ones that are structured enough to belong in an outliner, and ones that I capture using Mac OS X services."
"If you want something more powerful and versatile than Notebook, try DEVONthink, DEVONthink Pro, or DEVONthink Pro Office. One of the most popular academic productivity applications on the Mac, DevonThink Pro accepts most file types including video and audio, web pages, pdfs, etc.; even rss feeds. It is a digital commonplace repository for multiple file formats. If you want to juxtapose your own rich-text notes with live web pages, pdfs, images and multimedia, then DevonThink is the answer. DevonThink also offers artificial intelligence assisted classifying and searching of notes (watch the demo videos and video tutorials to see how powerful and easy-to-use the AI searching and classifying features can be). Selected text in DT can be linked to specific notes, and wiki-linking can be automated. Devonthink supports advanced Boolean and proximity searching. It's easy to import text, clips, urls or other items to Devonthink using the Sorter tray, accessible any time from any application. Exporting is rich and versatile. Multiple databases can be open at the same time. DT has great support for AppleScripts, Automator, OS X Services, and other Mac OS X technologies. The Pro Office version supports high-quality ABBYY FineReader-based OCR conversion of pdfs. In one trial of an earlier, less powerful OCR engine, I imported a pdf I obtained through inter-library loan which contained poorly photocopied pages with different fonts, and a mixture of single pages and double-page spreads. The OCR conversion was surprisingly accurate, automatically rotating pages as needed, and in a comparison it was much faster than the OCR in Acrobat Professional. I use DevonThink Pro Office as my chief research tool, for note-taking of print and pdf sources and for online searching."
FYI--This information is about 3 years old and helped me in my search for Mac apps to help in my academic workflow.