For my own memory, I'm listing things that upgrading to El Capitan broke in my dev environment. (All these were working before the upgrade.)
I will likely come across other weird behaviour that I'll have to fix, but suffice it to say, the main headache was having my various Apache customisations blown away and then having to figure out what to do all over again.
(Discovered this several days after original blog posting)
It turns out you are using an outdated browser and my site might look a bit weird for you. (images are off colour, text gets cut off, layout is wacky) This is because your browser does not implement web standards. Please consider an upgrade.