I use many house rules in my game.
1) Modified critical hit system. I took the Hackmaster critical hit system and converted it to 3.5. Very cool.
2) UA's alternate wound system. Basically, it eliminates the -10 floor, and substitutes a fort save when you reach 0 HP.
Bascially, the first two are designed to replace lethality with serious damage. The HM crit tables have been modified so that instant death is very rare. However, serious lasting injuries are more likely. So instead of x3 damage (and perhaps a death) you end up with -2 Dex and a 25% penalty to movement as your left knee tendons have been ripped from the bone! Combined with the fort save (which also reduces lethality) you end up with a system that reduces character death while still preserving the danger of combat. Besides, it's cool when your character has permenent scars, or perhaps is missing a finger or two!
3) Contested Tumble and Concentration checks. This repalces the standard DCs. Basically, subtract 10 from the standard DCs and add back the melee attack bonus for the primary weapon of the enemy. It should be easier for your 10th level monk to tumble past a goblin than an ancient red dragon! Same for making concentration checks!
4) Continuing damage for poisons. Basically, the normal rules for poisons apply. After damage is rolled and appled for both primary and secondary, the continuing damage kicks in. Once per minute another save is made for each remaining potential point of damage remaining. In other words, say a poison does 1d6 STR / 1d6 STR, and a 3 is rolled for the primary and a 4 is rolled for the secondary damage. The maximum possible damage was 12, and 7 has been taken. That means over the next 5 minutes, one save must be made each minute. Passed saves skip damage, and failed saves result in one more point of damage taken. This does make poisons more dangerous!
5) Rich Burlew's modified Diplomacy rules. See
http://www.giantitp.com for more!
6) Toughness feat applies +1 HP per hit die rather than a flat 3 HP. This feat as written is useless to everyone. This modification makes it useful again. However, since Con boosting items provide a similar bonus, characters with limited feat selection will probably still shy away - unless a significant number of HP is desired. Even at 20th level, this provides 20 HP - which is usually less than a single hit taken.
7) More dangerous falls! In addition to the standard damage, the character must make a fort save of DC 2 per 10 feet fallen, or become Dying (see #2 above).
8) Magic Rating from UA. This helps multiclassed magic users stay viable at higher levels. Otherwise, a 20th level character like a 10th level bard / 10th level wizard would be as effective as two 10th level characters - who could only each take an action once every other round.
We also use Reputation and Contacts from UA, as well as the critical fumble rule from the DMG (with the addition that creatures with no weapon to fumble must make a DC 10 dex check or fall prone!)
In addition to those, I use many other rules for things that aren't really covered in-game. Like a system designed to provide a DC for those seeking magic items or scrolls. I can go into more detail of that system if anyone is interested!