I just bought a guitar off of Ebay, and was asking this same question last week. You guys gave me some great advice, and after playing the guitar, I concur and I'll repeat it here.
Duncan Designed pickups are not very good. The ones I have in my new ESP 7-string are very dull sounding. This guitar, which I've set up to be almost identical to my other guitars, has a much duller, less crisp sound, and it's mainly because of the pickups. I'm having new pickups put in this week, and I would strongly advise going with some high-end DiMarzio, or Seymour Duncan pickups. You might want to check out EMG pickups as well. They're not really my thing, but active pickups may suit you if you're going for a super-heavy sound.
DiMarzio Tone Zone
Seymour Duncan JB trembucker
Seymour Duncan BS trembucker (some wicked cool pole pieces and a fat, old-school sound, I have one of these in an old Ibanez, it's a perfect pickup for a de-tuned sound)
DiMarzio Air Norton (bar none, the best neck pickup IMO, it's extremely percussive and gives your fast alternate-picking lines EXTREME definition.)
I love DiMarzio neck pickups and Seymour Duncan bridge pickups.
one more thing...........