Clerics: Since there are no "active" gods, you may choose any two domains of your choice. (Even opposites; if you can justify it in your background, I'm willing to let you play a cleric of Good and Evil, or Creation and Destruction.) And if you'd like to use a non-standard or custom domain, send me a note; I'm pretty flexible, as long as the powerlevels stay reasonable. You are essentially a cleric of a philosophy.
Other divine spellcasters: All class abilities work normally.
Druids: The weapons restrictions are void. You start with proficiency in the weapons listed in the Player's Handbook, but if you acquire proficiency in other weapons (through race, a feat, or multiclassing), you may use those weapons without losing your druid powers. However, you still may not wear metal armor, or use a metal shield, without losing your powers.
Paladins: You may multiclass, as long as you remain lawful good and true to your code.
Rangers: I use a slight variant. Three changes:
Monks: I use Oriental Adventures rules, which permit multiclassing, add a little flexibility in feat choice, and add several weapons to the "monk weapon" list; contact me if you need details. In addition, you may spend a feat on a "Monk Weapon Proficiency", which allows you to treat a melee weapon of your choice as a "monk weapon" even though it normally is not (eg. naginata, longspear, longsword) -- it becomes part of your unarmed martial arts style. If the weapon is a martial weapon, proficiency is included for free. If the weapon is an exotic weapon, you must also spend a feat on Exotic Weapon Proficiency.
Skill Focus: This feat provides a +3 bonus to the skill, not a +2.
Elemental Substitution: Sonic substitution is not available to sorcerers, wizards, or druids. Clerics and bards may still use it.
Elemental Substitution II: When a spell is first available/learned, the spellcaster may choose an elemental-substituted version instead (eg. Acidball instead of Fireball). An energy version of a force spell (such as a lightning-based Magic Missile) may be learned, but not a force version of an energy spell. The character may learn only one version of the spell, unless he has the Elemental Substitution feat.
Tumble and Concentration skills: When using these skills to try to avoid an attack of opportunity, the DC is not flat; instead, it varies according to the base attack bonus of the creature threatening you. A 20th-level fighter is harder to tumble past than a 1st-level fighter.