I nominate 57/08 pickups as the best pickups PRS has ever made, in fact they are the best humbucking pickup ever made by anyone (including vintage PAF). I've played guitar since the late 60's and have owned several vintage instruments along the way but nothing sounds as sweet as the 57/08's.
The worst for me has been the HFS, I bought several PRSi in the 90's and ended up selling because I couldn't bond with the HFS + the five way rotary switch. The HFS was to hot and bright for my amps and when I would dial down the volume it seemed to get thin. I would be curious to know what pickup PRS has sold the most in the last couple of years.
(Sean, can you give us that info?)