Most of my house rules are more setting-background related than mechanics related, but sometimes they tie in together.
I use core 3.0E as base.
Spells are banned or limited so I get the game I want:
- Teleport spells are only accessible to a NPC prestige class like the wayfarer. Dimension door, which is available, requires line of sight to the destination. If a party needs to travel great distances in a short time they can use portals, but those are often in remote and dangerous locations, and not always working - basically, DM controls when such portals can be used.
- Raise dead and similar spells are banned. Though players can expect that their PC will not get killed without a warning and a way out (even if that way out may be "surrender and get captured".)
- Divine Power and other spells that make a cleric a better melee fighter than a fighter are banned or reduced in power.
- Haste is banned.
Some feats are banned as well.
Anything (spells, feats, prestige classes) from splatbooks and other books gets approved on a case by case ruling - what is ok for one PC might end up unbalanced with another PC, or party.
Setting-wise, I play in the Forgotten Realms, but they are darker than the book version.
There are much less magic items around. There are no magic item shops, and magic items tend to be powerful, and with their own history and plot hooks, and growing in power/unlocking their true power through quests or other adventure-related processes as their wielder grows in power. No "I commission a +3 flaming shock longsword and have my plus 2 armor upgraded". So, PCs tend to have few, but powerful magic items, not a plethora of utility items. Scrolls and potions (low-level ones) are fairly common though, but usually not sold to just anyone, but hoarded for allies and members of the church who made them.
There is less treasure to be had by adventuring. Orcs, bandits and monsters haven't hordes of gold around, and an average adventurer does not make more gold than an average mercenary. Real money is made by nobles (through land and taxes) and merchants, not killing creatures and taking their stuff. In fact, I don't bother with exact gold and treasure amounts anymore - PCs can afford a certain lifestyle, with all it entails, or not. Since you can't order magic items, most of the reason to require a detailed amount of treasure is already gone anyway. Rewards like lands, titles, trade rights/monopolies are used to grant "lifestyle upgrades".
The realms are far less egalitarian than their official versions. If you are not a noble (or a filthy rich merchant in a land without a strong aristocracy) you are not worth much in lands with nobilty in charge. Serfs are slaves in all but name, and their use is widespread in the north, and in the heartlands. Slavery is common in all southern countries from Calimshan to Semphar.
There are few if any good rulers - most have to compromise their morals to rule a country.
There are few if any evil or good people - most are neutral. Good/evil people are usually religiously motivated. A bit of altruism alone does not make anyone good, nor does killing someone make anyone evil. There are no "good races" - only neutral ones. Same goes for evil races, but those are usually under the thumb of evil priests and traditions.
The humans are the dominant race. Elves and dwarves are on the decline. No thundertwin event, no "return from retreat".
Elves have a stagnant culture, rooted in age old traditions, unable to change fast enough to keep up with human innovation. Their items are still some of the most beautiful, but their magic has been surpassed by human zeal for innovation and risk taking, especially in Halrua, who added 1500 years of arcane research to the 3000 years of magical research of ther Netherese ancestors, and in Thay. Elves still have the reputation to be the realms' best and most powerful mages, but that is not true anymore (and part of the reason they hole up in Evermeet, and keep non elves out).
Dwarves are dwindling in number through low birth, and high losses in wars. They are the best metal and stone workers - elven steel may be prettier, but not better, and elven smiths never really went beyond chainmail and longswords - but again, humans are catching up.