My 2 cents...
I had a hardtail Ibanez S-series that was made of mahagony and it had a Duncan JB in it. I really liked the sound, but I sold the guitar and decided to put the pickup in a Jackson JJ which was either basswood, alder or poplar. After I put it in the pickup sounded terrible and almost microphonic, so I took it out and vowed to never put it in another guitar that wasn't made of mahogany. Point being is that the type of wood that the body is made of contributes to the tone, in addition to scale length and being bolt on, set neck or neck thru, and how much sustainable wood there is (ie. hardtails vs tremolos & swimming pool pickup channels vs. direct mount pickups).
My personal choice is Duncans and I'd recommend in the humbucking position the JB or the Invader, which is very good on a dropped tuned Les Paul. I use the Classic Stack single coils on my Strat because they are clean and noiseless and look like Strat pickups--although the Quarter Pounder I hear is good for matching up volume levels of the pickups. I also like Duncans because they have 5 wires and you can do lots of coil tapping, phase stuff, etc. with your own soldering gun.
If you are after heavy metal/rock, the EMG's are pretty good for just that too. But if you are getting a set of EMG's (H-S-S) I'd make the humbucker an EMG89 which is an 81 that can coil tap to a single coil sound. This way it'll give you more switching possibilities. If I remember correctly EMGs run off batteries, so if you are the type to leave your cord plugged in overnight, you'd better invest in some 9-volts. Also I think EMGs have that plug and play system, so that you dont have to solder anything. Good for the average joe, but bad for guys who like to coil tap and hotrod their electronics.