Just thought I'd throw a little more mud onto an already cloudy situation.
All pickups have different tones. It's a personal preference. Some prefer a certain type of magnet, or type of wire, or number of windings. Single coil, humbucker, P-90, are all different types of pickups that have inherently different tones as well. It's hard to recommend something without knowing what type of guitar, style of music, type of amp you're using.
The hotter pickups will push the tubes more, i.e. more distortion. So conversely, the cleans won't be as, er, clean. Not that it's a bad thing. It still depends on what you're going for tone wise.
I personally am using an SD Jazz in the neck and a SD Custom in the bridge of my EPI Les Paul Custom. The stock pickups were too muddy. Kinda warm but lacking definition. Most aftermarket pickups will be an improvement over stock. From what I've heard, the Duncan Designed pickups are not as good as the original Duncans.
Here's a website that has tons of info and also sells Duncans, DiMarzio's, Lindy Fralin's and Bill Lawrence pickups.
http://www.torresengineering.com/index.html
Hope that wasn't too confusing.
OP