Re: SD Low End
I'd say the PATB-2 Parallel Axis Distortion is one of the fattest that can still pull off palm mutes. Highest output of any of these pickups, though all of the ones mentioned in the thread so far are more than enough to get the high output pickup into hot preamp thing going. PATB-2 is an amazing gonzo metal pickup, though lacking in subtlety for cleans and low gain. Surprisingly nuanced for high gain leads, though. Screaming harmonics and incredible sustain, not just from the high output (though it is one of Seymour Duncan's hottest pickups), but from the lower string pull. It's also odd looking, and slightly wider than most other humbuckers, which can be a problem in guitars with tight routes. I love it for metal riffs and leads in particular. My first choice for a metal pickup.
The Invader is deeper, but has enough bass to be problematic in some amps. Though Synyster Gates manages to get some suprisingly JBish tones out of his for leads when he wants.
Alternative 8 is deep but tight. Different upper mid focus than the others.
Black Winter is very popular now, it's similar to the standard Distortion, but relaxes the upper mid focus a bit and is more flexible.
Nazgul is particularly suited to some styles of metal, but is probably the least flexible pickup of the ones discussed. Specialist, but great at what it does.
Custom is punchy and chunky, but doesn't have the same cutting upper mids as everything else that was suggested. Great rhythm pickup (Dave Mustaine used it on Symphony of Destruction for rhythm, an unusual departure from his near-constant JB use). Not bad for leads, but harmonics don't scream out quite the same. More flexible for cleaner and low to mid-gain tones, too.
I'd probably focus on the PATB-2, Alternative 8, Black Winter and Custom. PATB-2 is hottest, followed by Alt 8, then Black Winter and Custom are fairly close in output to each other but very different sounds.