My Explorer is heavy and dark sounding, as well - but I'm going more for bluesy and rock type sounds myself.
It's had Riff Raffs in it, which were initially very nice in there, but the guitar made them a bit nondescript to me. I swapped my Mississippi Queens into her, and I'm a happy boy. I now love the "dark" part of the guitar now - she's a lovely rich, warm, and expressive beastie, but with plenty of bite when I want.
I think, for me anyway, the bottom end was a bit too much for the RRs, and was drowning out their mid characteristics. They sounded fine, but so-o much better in an SG I have now.
Now, for what you want... while I was wondering what to do with my Explorer, and even considering letting her be the metal-monster that the 500T etc was suggesting, I got some suggestions from folks on here, and Painkillers or Warpigs seemed to be popular for a dark/heavy explorer. Of course, nearly every other BKP hi-output humbucker was also mentioned :lol:, but Painkillers and Warpigs (A5) seemed to be the favourites at the time.
It will be interesting to see what gets suggested now :D