I have a lot of minor house rules, but here are some of my more *major* house rules:
-Worn armor (actually armor, not natural armor, not Mage Armor, etc) gets an armor check against criticals. If you are wearing armor and get hit with a critical, roll d20+armours base bonus (e.g. +4 for chain shirt, +8 for full plate, etc). If this totals 21+ then the hit does normal damage. You get 2 checks if you also have Fortification. (This was done to make wearing armor more "appealing". I found that because of the limitations of armor, everyone (even Barbarians) are wearing bracers more often than armor)
-Spells which give random temporary hitpoints (Aid, False Life, Heroes feast, etc), just take the maximum instead of rolling. (I hate having piddly rules like rolling for temp hit points when a set number is fine.)
-Toughness feat is +1 hit point per level and it stacks if you take the feat more than once. (the +3 hit points was too weak and the more hit points characters have the better)
-Hobby skills. Every character gets 3 skills, chosen at level 1, that advance automatically at maximum ranks. I made a list of skills that players choose from that represent skills that could be a "hobby" or even a second profession. Skills like Appraise, Climb, Knowledge, Profession, Survival. These skills automatically advance at full rank and are considered 'class skills' for that character for all intents and purposes. (this was done because I felt that some classes were lacking in skills. Players were not taking skills like appraise, knowledge, etc because they needed to spend skill points on skills they would be using the most often)
-Clerics can spontaneously convert existing spells into any spell in their domain spell lists. This works like their ability to spontaneously convert spells to "Cure" spells, but they can do it for any of the spells in their domain list as well. (this was done for flavour)
-Specialist Wizards can spontaneously convert and cast spells in their specialist fields. For example, when an Evoker prepares their spells for the day, they dont have to prepare any evocation spells at all. Instead, then can just spontaneously convert prepared spells to Evocation spells. (this was done to make specialist wizards more appealing).
I've decided to only use house rules to add to something that I think is lacking or needs balancing. I found that adding too many house rules for "flavour" results in too many house rules. I figured that if I wanted to go with house rules for a lot of "flavor" items, then I would just make up a campaign setting.