After reading your comments to my last post I remembered another aspect of the rules on my shortlist: they often deal elegantly with an issue that DMs have been fussing and fighting with for years.
I think these are often the places that D&D is just a little too abstract for most people. Examples are critical tables and skills. Since the moment I was told about D&D, I've seen people reinvent those wheels a hundred times, trying to find a sweet spot between playability and satisfying detail.
Remembering this, I thought it might be a generative way to think of great house rules: what areas are you, and DMs you've seen, constantly house ruling. Which rule sections are almost guaranteed to get house ruled or have a question asked in a forum "How do you handle . . . ?"
I'm thinking two things might result from this 1) you may see someone commenting on X always being troublesome and remember "Hey, Joe Blow's rule really handles X well." 2) In the back of my compilation I could put a section called Requests, sort of millennium challenge for awkward D&D bits.
So, what always gets house-ruled?