I'm going to be changing out my pups in my PRS SE. It currently has a EMG HZ(terrible) and the stock bridge pup. Seeing as I already have a Hellraiser with EMG 81/85 I want something with a different sound. Something that will still have the bite I need for metal, but that will be able to give me some more organic sounding cleans. Your turn, go.
So this is just me but I would get a passive pup. I like my Duncan Custom Custom. More brown sound than br00tlz but you get get teh metalz too. Maybe the newer SH15 Alt 8. I know Pott has one. I searched on it real quick and found this kick ass thread by Pott.

DiMarzio Super Distortion might be something to look into.

Esp/LTD JH-200
Ibanez RG2EX2
Yamaha FD01

Marshall MGDFX250 (It was a Gift)
Peavey Vypyr 15 watt

Digitech DF-7
Look into the Seymour Duncan Distortion Mayhem SH-6 set. I have Seymour Duncan hot rodded pickups on my les paul and they sound amazing, they really improved my cleans ans well as made my distortion clearer and louder. I imagine that the distortion mayhem set offers a more metal feel than my set, which is probably what you are looking for.
seymour duncan jb 102 i think they are ..the jazz ones are pretty sweeet or put burst buckers
bridge pup - Dimarzio D-sonic
neck pup - Dimarzio Humbucker From Hell
My Gear
-Gibson Les Paul Studio
-Ibanez "lawsuit" Les Paul
-Ibanez S470
-PRS SE Custom

Marshall TSL100
Marshall 1960a cab

Dunlop 535q wah
Visual Sound Liquid Chorus