Favorite: changing the way xp works for 5E. Monster xp is cut in half, and various exploration and social encounters make up the difference, with possible quest xp for completing the objective. I feel a little bad about using this one as my favorite, because it's mine, but it's also probably because its from the most recent edition (I played with a LOT of houserules over the editions).
Least Favorite: Critical Hit/Fumble tables. Most people complain about the critical fumbles, but I hated the critical hits more. Dismemberment in AD&D was far harder to fix, and stupidly common with these charts. I remember one 2E game where my sword arm was cut off, with the sword knocked into a pit, so I had to pick up my own arm and beat the orc to death with it.