This site is currently running WordPress, hosted on Dreamhost, using a one-click install. I’ve tried a lot of (flat-file) content-management systems and that would be my preference, but alas, here we are.
Many of the photos are duotoned with #faf9f7 (white) and #1e8449 (green) or #0d6c36 (darker green). Thanks to Dominic Prestifilippo for suggesting shapefactory.co and for the recommendation on the white-variant.
I wrote a simple R-script to generate the featured image for my papers, which pulls from a PDF version of the paper.