Its hard to say which are the best:
the Paladin and the Warlock PrC in the Warcraft RPG are good ones though.
Some of the absolute WORST PrC classes can be found in the Swashbuckling Adventures book, their power level is vast in a way that would make epic characters gasp with horror.
Nacht Assassin: one of my players, as a joke, min/maxed a character using this PrC. Not having access to any magical weapons the tenth level character did around 700 points of damage in a round.
Drexel Swordsman: the party Tank took this class, and became nearly unstopable.
there was another PrC in that book that focused on combining dancing with large curved swords that was capable of dooing 100 points of damage, repeatedly in a round.
