Supplementing this posting from last year … I’ve changed how I do things.
Most of the time I view the web page in Safari Reader view, then Command-P to print dialog, pick “Save PDF to DEVONthink 3” which puts the PDF into the “Inbox”. If that view not good enough as sometimes all graphics don’t display–don’t know why–I do same with the native page view in the browser. I sometimes add tags.
Periodically, daily or weekly–whatever–I drag and drop numerous PDFs into “PDF Squeezer” and batch compress them. Mostly using “Strong Compression”, but where graphics are needed, I used “medium”. Does a good job. I don’t care with Strong Compression photographs sometimes are very fuzzy. I always have the source URL to get them if I need them for a presentation or something. Then save them back to same location in DEVONthink (Inbox).
Periodically, daily or weekly–whatever–I use “See Also & Classify” inspector to everything still in Inbox and move them into appropriate DEVONthink database/groups, replicating where it occurs to me. I sometimes add tags.
I’ve grown to prefer PDF’s rather than Markdown because all the graphics are inside the files, reading and annotation tools are easier, especially in iPad where I do most of my reading of these files. Yea, I know others use Markdown because “easier”, and again I don’t care and won’t try to impose my will on others. Just passing on what I do in my world.