The single biggest thing I've houseruled on is a general prohibition against save-or-die effects on both sides of the screen. This was mostly to protect the players. For example, they used to think it was bad-assed to throw out
disintegrate left and right... Until they ran into a beholder.
Some players have been pressing me to integrate Heal checks in a way similar to Spot checks, to allow characters to tell how hurt their party members are at a glace. Apparently, some local groups are already doing this. I don't dig it so I haven't added this yet.
I don't roll for hit points. Everyone (players, NPC's and monsters) get full hit points on their first die and half max +1 on every hit die thereafter. This is because I've seen a 6th-level cleric with 22 hit points.
I also allow all characters to make untrained Knowledge (local) checks for their home region. I figure this is logical, because chances are that you know at least the basics about your own homeland.
Although it's more procedural than a house rule
per se, I also have initiative rolled at the start of the session. This lets me start a fight with a surprise instead of giving the players the cue that it's about to hit the fan.