Yes indeed. As @DTLow mentioned, DEVONthink handles PDF files very well – I would say PDFs are its forte. I personally use it for managing academic papers and books, almost always in PDF format, and have been very happy with the way it works. It has great annotation facilities and powerful search features, and I especially like the PDF viewing/annotation experience on an iPad. I index some (relatively short) videos in DEVONthink too.
A couple of quick notes:
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Some PDF books are protected, and this can interfere with doing things like highlighting and annotating them. It is sometimes possible to “jailbreak” them using techniques that probably shouldn’t be described here, to avoid legal issues, but can be found on the net.
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A current weakness in DEVONthink’s PDF features is the lack of a bookmarking feature similar to what you would fine in something like Kindle. You can work around it, for example by keeping a file that has links to specific pages in a PDF, or (what I do) come up with a convention that involves putting a mark somewhere on the page in a corner so that you can visually see these literal “bookmarks” when you use the PDF page overview in DEVONthink. The photo below shows an actual example – look closely at the middle row, the left-most two pages, and note the blue squares around the page numbers. I simply use the drawing tool in DEVONthink To Go on the iPad to create a square with thick borders. Yes, it’s hokey and not ideal, but as a cheap way of doing it until DEVONthink has better bookmarking features (hopefully, some day), it works for me.
