With the available WUs, Intels will produce max ppd. For just about anything but folding the FX-55 is the best out there. When, as Frank mentioned, FAH adds AMD SSE2 support to the QMD core, I expect the FX series to again be the king of the folding hill. In the near future, Dual core Intels promise to produce very good ppd (maybe as much as 700 ppd on big WUs) but they are very bandwidth limited. For folding, the Dual Core AMDs are going to be THE killer cpus in single and dual cpu configurations.
Today, the folding performance of the Intel and AMD cpus is close enough that the answer to which is best depends on what WUs are available or folding one or two instances on HT rigs.