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I am not exactly a typography nerd/connaisseur, but I must acknowledge that the choice of font, text-size and related properties can indeed have a huge effect on the perception of a website. This is especially true, when the site is generally text-heavy.

Two recent examples, where the choices typography (in conjuction with the content itself!) impressed me were The enchanted electrical website of Dr. Sinclair and Beyond the Frame. The latter makes use of Tufte.css, which includes the et-book fonts. The former has a wonderful explanation of font choices in its colophon, to give the gist: Munson for body text, Rosewood Std Fill for headings, Courier Prime for code, and Franklin Gothic FS for sans-serif.

And while I admire the results, I don't like the idea of needing to load webfonts, which then dwarf the actual text content by at least one order of magnitude. I chose to rely on system fonts, which nowadays can get you quite far as well. I recently found the Modern Font Stacks overview page, which offers some advice and previews for what is possible with a single line of JS without any further need for network requests. I tweaked my previous choices a bit and now use Didone stack, although I removed the "Bodoni MT" option from it.