I offer two insights.
(1) It seems to me that there are two types of houserules. First, a DM changes an existing rule that he does not like for a rule that he does. Thus, if I dislike the absurdly easy rules for sundering an object off of a player, or if I think that not being able to overrun on a charge is stupid (both rules I would be tempted to change), I alter them.
But there is a second type of house rule: a rule that one simply does not use because it is too complicated. Here the objection is procedural, rather than substantive: the rule as written is simply too time-consuming and impractical to be used. A great example of this are the endless and idiotic rules on terrain types (wait, I'm in a forest, I move 1/2 speed, get +2 on my armorclass? Or is it 1/4 speed, get a +4 on my...aw, soddit).
If I were to advocate houseruling (I do not, see below), I would think that procedural houserules would improve the game, while substantive houserules would not -- whereas a procedural change makes a rule useable that wasn't before, a substantive change merely alters the outcome to one that the DM personally prefers.
(2) I'd also like to offer the following justification for no houserules. I believe houseruling rarely -- if ever -- improves the game. The game is playable as is. Therefore, nothing specific is required to make the game playable. Each rule change is an alteration of the expectations of how the game usually works out. Players rely on this. Their past experience teaches them smart moves for the present.
In short, humility is in order. I think I can improve the 3.5 rules. I hate the changes to Paladins. I think the sundering objects rules are just dumb. I think not being able to overrun on a charge is silly. There are a few others.
But can I really guess better than the accumulated experience of the players of this game, as encoded in the RAW? The RAW are a product of thousands of campaigns. I have 20 years gaming experience. The RAW represent hundreds of thousands of times that.
To vindicate player expectations, to prevent the DM from upsetting the game over personal preferences, and to give everyone a sense that they are not just writing a communal novel, but are playing a game, my inclination is to use no houserules at all.
best,
Carpe