My only major houserule is my variant XP system. I dislike kill XP just for slaying monsters, and so I adapted a more story based approach a la GURPS or Shadowrun. Basically, it goes like this:
1. After each play session, individual PCs are rated on a scale of 1 (poor) to 10 (outstanding). I do this by giving 1 point for player attendance, and then 0-3 each for danger, achievement, and roleplaying. The average should be about 5 rating points per session. (Characters who are run as NPCs due to player absence only get 0-3 points for danger.)
2. The rating is multiplied by a scaling factor based on average party level, namely
(APL + 1) x 50 XP
The recommended rate of advancement would be APL x 60 XP, but I like faster advancement in the early levels and slower later.
So far, this has worked out quite well. We can do roleplay-heavy sessions and no one complains that there is too little advacement. And we can do combat encounters in a smart way, i.e. no "one more goblin to level up" syndrome.