All I can think of right now that we'll be house-ruling:
Several skill changes. I am flabbergasted that Jason B. considers a rank of Stealth, a rank of Perception, a rank of Acrobatics, and a rank of Swim to all have the same in-game value. They are wildly disparate. The skill decisions made, IMO, are the only truly weak spot in Pathfinder.
Disabled/Staggered. In our games, Disabled/Staggered has a range equal to your Constitution mod. (So an 18 Con PC is disabled when between 0 and -4 HP, inclusive. An 8 Con PC is disabled at 1 HP!)
We'll have other changes, but those aren't so much house rules as "atmosphere" rules. (Like making coming back from the dead more difficult.)