I run mostly Eberron, but I constantly tinker with mechanics. Nearly every monster or enemy is a unique creation. I have also revamped many of the classes, feats, and spells. I just about recreated the Artificer from the ground up, have my own version of warforged, shifter, and changeling, and a number of new archetypes, feats, and spells.
EDIT: Oh yea, I forgot I make unique magic items and boons to grant my players, a different HP system, changed the way critical hits/fumbles occur, and include my own version of action points.