Depending on your preference of pickup type (ie. Jazz pickups, P pickups, MusicMan style pickups)-
I've used the Seymour Duncan Quarter Pounder P- bass pickups: they are fantastic, very solid low end and low midrange but with more highs than comparable P pickups as well. Steve Harris from Iron Maiden uses these. They sound good to me either clean or dirty, some people describe their sound as "scooped"- but I've found them to have plenty of great midrange growl even when EQ'd flat.
For Jazz pickups- alot of guys use EMG active pickups for metal, I guess for the same reason that alot of guitarists do- they have a decent frequency response, but more importantly they make no noise and feedback less than typical passive pickups- if you want really clean scooped mid type tones, you'd probably dig them. I actually don't like super clean metal bass tones though I used these pickups for about 2 years- so my pick for Jazz pickups are the Dimarzio Model
Js: they are tonally about the opposite of the EMGs, with very heavy midrange (and a great low end) and can sound really dirty/ nasty in a good way, especially through all tube amps!
For MusicMan style- I have only used a Seymour Duncan MM Replacement pickup (I believe its an Alnico one) and it sounds great- deep lowend/ + midrange punch and really glassy highs, it seems the most versatile in the sense that it can be both really clean and hifi sounding or really dirty depending on how you EQ it (I have only used it in a bass with an active EQ, so I don't know what it would be like in an all passive bass).
My favorites so far are the G&L MFD humbuckers: they are the thickest of all that I have used and sound especially good through tube overdrive, the only better pickup for the overdrive that I have tried is the Dimarzio Model J- but the Model J doesn't have as much output or as much punch. The G&Ls are kind of like having 2 Model
Js in one pickup in my experience! The only downside to them is that I don't think you can buy them seperate of G&L basses, but if you could ever find some I would highly reccomend them!
I also reccomend wiring any pickups you try in series (or installing a switch to have either series or parallel wiring)- Ever since first trying it out on my bass with the Dimarzio Model J pickups, I've installed a switch on all of my basses: series wiring offers more low midrange punch generally and extend the low end to some degree as well, which works well if you like dirty, midrangy metal bass tones as opposed to clean, scooped- midrange tones. Although I guess you may not like either of these- they are just the most common metal bass tones that I hear these days.
My late-night 2 cents....
Karl Zickrick