I say, "90% or more as written." In my current Eberron game, I have a few:
1) All “orb” spells are evocations instead of Conjurations, and thus spell resistance applies to their use. WHY: Almost completely nullifies spell resistance and makes evokers almost obsolete.
2) Feat Double Wand Wielder from Complete arcane uses 1d4 charges per extra activation instead of 2 charges extra. WHY: Overshadows Cannith Wand Adept Prestige Class from Sharn City of Towers book.
3) Price for Drow Sleep Poison Doses raised to 750 gp each. WHY: Vastly underpriced for the effect.
4) Purple Worm Poison raised to 1000 gp each. WHY: Vastly underpriced for effect.
5) Eliminate “Damp Power” from Complete Psionic. WHY: Too low a cost which completely defangs targeted and area-effect damaging spells.
And as it stands, that's all. Everything else is book-as-written. If I add any future house rules, I allow my players to re-write the characters to make another choice, if so inclined.