I used to run my games in a highly modified combination of 3.5, stuff from UA, and pure houserules. But, about a month ago (or maybe less...I can't remember), I switched over to Grim Tales.
So, the only houserules I use now are...
2 extra skill points for Strong, Fast, and Tough,
UA armor-as-damage-reduction,
Customized WP/VP system,
A few homebrew races,
Ad hoc (i.e. 'made up on the fly') XP,
and a few minor modifications on feats and so on.
This works out quite well, since my campaign is Subtle-Magic (not to be confused with Low-Magic), Grim-but-not-Gritty (hence the WP/VP), and doesn't have a lot of dungeons. So far, in the three adventures I've run, only one had a dungeon, and it was a relatively small cave.