According to Dave Weiner, the lower output the pickups are the tighter, less muddy your sound will be. He reccomends the PAF 7. I wouldn't argue with that guy, he KNOWS his stuff lol
My experience has been (and I'll admit, it's pretty limited) that generally high output pickups tend to be concentrated in a pretty narrow frequency band. They sacrifice even-ness and depth for a really high spike to really drive the front of an amplifier. This could be because of the pickups themselves, or a product of tube amplification, where as the tubes overdrive they tend to compress, so whichever part of the input signal is hottest will tend to dominate the preamp.
So, a lot of very high output pickups I've played - EMG's, DActivators - tend to actually sound pretty tight under loads of preamp gain, simply because the less powerful sections of the signal are being effectively compressed away to nothing.
The flip side is that lower output humbuckers to me always seem to sound more expansive, more balanced, and more even. At low to medium-high gain settings, that's great - you get a very broad, full, and singing tone. Jack the gain up into the stratosphere, though, and since the signal coming in is less "notched" than a higher output pickup, the whole thing gets reproduced pretty evenly and you tend to get a flubbier low end.
So, this is why something like a Duncan '59 will sound absolutely heavenly through a singing mid-gain distortion sound, but gets a little woofy when you saturate the hell out of the signal, whereas an EMG or a DActivator in the neck will be a bit thinner and snappier in the former settings and just won't have the same "balls" to the tone, but will remain articulate under gain settings that render the '59 a giant soggy ball of sheepskin.
That's my experience, anyway, based on the handful of low and high output pickups I've played that I'm familiar enough with to comment on.
Of course, this could also be intentional on the part of manufacturers - no one buys a set of 707's to play Chicago blues, you know, while very few death metal guys probably buy '59's. High output pickups may be designed to sound clear under tons of gain, whereas low output pickups may be designed for fullness and articulation at lower gain levels.