I use a variety of variant rules.
1. I use an alternate XP table and XP rewards table. The rate of advancement is not static at 13.33 balanced encounters per level. It starts off very quick and it takes more encounters as the character gets higher in level. It takes about 3 times as many encounters to get to 18th level than normal, but PC's get to 6th level a little faster than normal.
2. Multi-classing is completely revamped. BAB and saves do not stack from different classes. Instead, it works like Gestalt from UA. The PC gets the best BAB and saves from whichever class grants the best bonus. This encourages single classing.
3. I award XP based on the a character's highest class level instead of the total character level. So, multi-classed characters earn XP a little faster than single-classed characters of the same ECL.
4. I use 12 skill groups which cover all the major skills. There are no skill points, only feats to advance the ability in each skill group. The feats allow a character's ability to move through four ability progressions with each skill group. All characters get a basic progression and it takes feats to get better. The progressions are level based.
5. I don't allow prestige classes. Prestige classes are turned into feats on a case-by-case basis.
6. I use spell points instead of spell slots, but I award spell points that are calculated based off the spell slots that a character would have. Spell points from various sources do not stack. A multi-classed character gets the best skill point total of all his classes.
7. Taint, Corruption, and Depravity from Heroes of Horror.
8. Traits from UA, Iron Heroes, and the Shackled City. Traits are determined randomly.
9. Sanity from UA/d20 Cthulhu. All characters have sanity resistance equal to 10+ their will save total.
10. Ability boosts gained at 4th, 8th, 12th, 16th, and 20th can be traded in for feats. But, feats cannot be traded for ability boosts.
11. Critical Hit Deck for PC's and Named Opponents.
12. Critical fumbles currently provoke an attack of opportunity from the defender only.
13. Massive Damage Threshold is equal to 10 plus fort save total. This is also the number of hit points a character can go below zero before dying.
14. Hit Points are calculated normally for the 1st nine levels. After that, characters get no additional Constitution bonus to their hit points and they get a fixed number of hit points per level. The amount is based upon hit die type of the class they advance in. The formula is HDtype/3 rounded down (d12=4, d10=3, d8 and d6 = 2, d4=1).
15. Most core classes from WOTC 3.5 hardbacks are allowed. In addition, core classes Monte Cook's Arcana Evolved are allowed.
16. Sorcerers get one additional spell known per spell level they are able to access.
There's probably a few more, but that's all I can think of off the top of my head.