Best: Spontaneous casting of Cure spells by clerics. Making clerics fun and desirable to play has had a bigger impact on the dynamics of my games than just about anything else. It's a rules change that has positive ramifications for the role-playing aspect of the game.
Runners-up: Damage resistance, metamagic, the new armor rules (ASF, Dex bonus, etc), named bonuses and stacking
Worst: Half-X templates for PCs. A munchkin's dream, and something that annoys me no end. I'll accept half-elves due to long exposure to the concept, and even grudgingly live with half-orcs, but this half-solar/half-dragon 12th level monk stuff just has to end.
Runners-up: Magic items/spells that boost mental stats, spiked chains, no facing in combat