In my Brotherhood of Rangers game:
Use my house-rule hybrid roll and point-buy system for ability scores, posted elsewhere
Characters are limited to one creature as an animal companion/paladin's mount/wizard's familiar, and can choose to take an extra feat instead of having one.
A bunch of travel/transport/teleportation spells are disallowed as not existing in the setting:
Air Walk, Astral Projection, Blink, Dimension Door, Ethereal Jaunt, Etherealness, Fly, Greater, Mount, Overland Flight, Passwall, Phantom Steed, Phase Door, Plane Shift, Refuge, Shadow Walk, Teleport Object, Teleport, Teleport, Teleportation Circle, Transport via Plants, Tree Stride, Water Walk, Wind Walk, Word of Recall
The 0-level wizard/sorcerer spells can all be cast at will, even by non-wizards who might have them as 1st level spells. Some of those spells have been modified/nerfed. In particular, they can't be recast until the previous casting ends.
Creatures larger than Medium have 5 ft reach; they do not get increased reach due to their increased size.
The Spot modifier for distance beyond 100 ft is 1 point per 100 feet (-11 at 200 ft, -12 at 300 ft, etc.) It's an outdoors campaign, and sight distances are longer than the RAW standard.
Creatures who speak Dwarven, Elven, Giant, Goblin, Gnoll, Halfling, or Orc will also be able to speak and understand at least a broken or pigin form of Common even if they don’t have Common as a “known” language under the standard rules.
Arrows have a 50% chance of breaking, being lost, or otherwise being unrecoverable whether they hit or miss, rather than following the RAW where arrows that hit are gone and those that miss have a 50% chance of being lost.
Monsters with poison damage will often have this altered to acid damage or will have the nature of the poison changed (e.g. to inflicting extra non-lethal damage). I find temporary ability score losses and boosts to be a PITA in the heat of play, and want to reduce them in the game. Although I haven't gone so far as to ban the ability score boost spells.
I'm still fiddling with Damage Reduction, because I don't like DR/golf bag, and it's hard to scale DR so that it's a handicap rather than a coin flip as to whether it's meaningless or overpowering.