1. Every character get 2 extra skill points per level, with quadruple at 1st level.
2. Toughness functions as improved toughness. You can't stack it.
3. No EXP points. With a spell that costs EXP, assume 1:5 ratio EXP/GP exchange rate for a costly material component instead. A 100 XP spell would cost 500 GP instead. This rule is a bit flexible since it breaks down in some cases but it's a good place to start from.
4. A alignment based smite counts as that alignment to bypass damage reduction. A paladin smiting evil bypasses DR/good, for example.
5. Dodge grants you a flat +1 dodge bonus to AC. You lose this bonus whenever you are denied your dexterity modifier to AC.
6. Monks get full BAB growth. Monk PrCs may or may not get this depending on the PrC, ask me if it comes up.
7. Paladins use charisma for spellcasting instead of wisdom. This reduces crippling paladin MAD.
8. Rangers get full animal companion progression instead of half.
9. I've been using a different turn undead in Balmuria and I like it, so let's use it here:
QuoteTurn Undead
You create a burst of positive energy centered on yourself with a thirty foot radius. All undead creatures in the area take 1d6 points of damage per Cleric level. A successful Will save (DC 10 + 1/2 cleric level + Cha mod) halves the damage. All living creatures in the area are healed the same amount (Will save for half, harmless). You are not affected by your own turn attempts.
Undead creatures with Turn Resistance take less damage. For each point of turn resistance, reduce the number of damage dice by one. So if a ninth level Cleric (9d6 turn damage normally) would turn a vampire (turn resistance 4), he would roll 4d6 damage less, so he would only deal 5d6 damage to the vampire.
Spells that grant a bonus to turn checks such as consecrate now grant an additional +1d6 to your turning dice. Some feats may need to be tweaked according to this, talk to me if so.
10. Sorcerers get Eschew Materials as a bonus feat at 1st level. They may use metamagic as a standard action instead of a full round action.
Feel free to suggest more or bitch if a rule doesn't do it for you.