I usually employed house rules for one of two reasons:
1. To add common sense to a rule set that lacked it.
2. To excise complexity from a rule set that didn't need it.
Pretty much the same here.
Since somebody else quibbled over the definition of "common sense", I might replace that with "rule that didn't make sense or was far from realistic"
I might also differentiate between "campaign rules changes" and "general rules changes". I have house rules for "how I run D&D" in any game I run. That's different from a specific campaign I might be running that has its own unique "world rules"
Generally, my house rules are intended to fix something I think is broken or to clarify something.
My house rules document generally details how I run my game, what I expect from players (any meta-game rules included) and then actual rules changes I might have from the RAW.
My 2e rules document was larger than my 3e document. In point of fact, I can't even think of what I changed in 3e, other than clarifying some stuff.
In 2e, I dropped spell memorization (making casters easier and more powerfule and adding variety to the spells used). I changed the rate of fire for missile weapons to be DEX based (bows were 2 per round in the RAW, I used DEX/6 rounded up).
When 3e came out, PCs got more attacks and the round was 6 seconds, not 1 minute, so the ROF rule wasn't justifiable. The Sorcerer changed the value of spell memorization, so to "support" the new class, we didn't carry over the no-memorization rule.
In that example, I modified the ROF for bows, because 2e D&D rounds were 1 minute, and it was unrealistic that an archer could only fire (and use up inventory) 2 rounds per minute. My change wasn't drastic, but it did make a high dex char feel better..
I dropped memorization, to simplify spell-casting and open up more options for players. Otherwise, PCs had long lists of spells that they never cast in adventures. Changing the rule increased the creative solutions seen at the table.
In 3e, I was pretty satisified with the design, so I didn't feel the need to tweak any rules. At most, I adopted Rich Burlew's fix for social skills, as he illustrated a design flaw that could be abused and his solution made sense and was simple.
One thing to reiterate is that I always have a house rules document that I start up for any RPG I play. Basically I try to capture any deviations we may come up with, so players aren't surprised. I also use the first section of it to outline how I run my game. In short, the document is the foundation of the player handout. I make sure I have something to give the player, so they know before hand how my game works.
This includes declaring how I expect players to behave at the game, and how we resolve rules disputes, contradictions and changes.
Its often surprising to find groups that don't do that. What's not surprising is to hear of those same groups having problems.