I had the same problem with my Jackson stock pickups. They were too muddy sounding so I went on a hunt. :D I ended up getting a pair of EMG 81/60 pickups (81/ bridge, 60/neck) and ought to say these are really great pickups.
Not sure if your into the active pickups or not, but these bad boys got rid of the muddy tone right away. Great sound, gives that nice Metallica palm mute chug that you always hear and KILLER for hard rock tones. It can nail cleans like a pro too.
I had been searching for the illusive "master of Puppets" clean tone for a looooooong while. I've spent literally hours in front of the amp and CD player trying to get the tone, but always was a little off or it sounded too deep. I threw the EMG's in there, and a couple minutes later had the clean tone I was looking for. (WOOT! XD)