It all depends on the sound and style you are trying to get. Anyone who recommends just one type of pickup, every time, probably doesn't know much about it, and is only recommending it because it's in his guitar right now.
I have tried a few different types, because I have played in several different kinds of bands, and enjoy different styles of music.
For Metal I prefer Dimarzio's... but that's for older styles of metal, like from the 80's and early 90's. For newer metal, I like SD Blackouts, or good ol' EMG's
For Rock, I like Seymour Duncan's JB/Jazz or JB/59 setup. This is a good setup for someone like me, who plays different styles, and is mainly going to be a rhythm guitar player. When I play lead, I like to use my guitar that has Dimarzio's in it, as I find it cuts through a little better... but for cleans, I love the jazz pickup.
PRS Dragon II pickups, and their McCarty pickups are supposed to be nice, as are Gibson pickups. I haven't had a guitar in them, so I'm not sure how they stand out, when compared to the brands I mentioned.
I agree with adam, it all depends on the guitar and what you want to do with it. My favorite guitar is an old Carvin with the stock M22 pickups they used back in the 1980's. Nice, clear sound when clean, overdrives well for rock and blues. Probably wouldn't be really greatest for metalheads, they are somewhere near PAF output but maybe brighter, it's hard to say because the guitar is maple, which automaticly makes it have more top end and definition than a Gibson.
I have a guitar with Duncan JB in the bridge and Alnico 2 pro neck. Nice and fat sounding and hot bridge, everybody uses JB's and the alnico neck gives a BIG difference when you flip the switch, and a bit more output than a jazz neck.
I converted an SG type to Duncan P-rails. When all the coils are on they are humbuckers with a tone that's all their own. Then you can split them. One coil is a P90, good old Gibson single coil, loud and fat. The other coil is HALF of a rails humbucker. Played by itself it pretty much is a strat type single coil. So add an extra mini toggle and you get 9 sounds instead of 3 with the pickup selector. The P90 sound is my fave, the others are really useful.
For something REALLY different I recently put some Guitar Fetish lipstick tube pickups in a couple strat type guitars. They sound much like an old Danelectro, but the mid pickup is a bit hotter and the bridge unit is a lot hotter than the vintave Dano units, plus they fit, and they are CHEAP. TWANG city!!! You still get some of the snarky in between sound of a strat, but with loads of pop and high end out of all three pickups. I put a set in a BARITONE strat (tuned B to B) and the sucker cuts through the mix without a trace of mud on the lowest notes. With some moderate distortion it's awesome. Think Led Zepplin;s Rock 'n Roll transposed down to E. Rumble power, but nothing like Korn.
For a "normal strat" I like Duncan Duckbuckers. No end to the quack. Add a JB Jr at the bridge if you want something with some lead power rather than just all vintage surf.
alot are good. i like the super distortion-dimarzio,because when you play at home the amp does not have to be loud and you get the tone your looking for. i just got a prs guitar,and it has awesome pick-ups too that come stock. the only thing i do not like about prs guitars is the volume knob is to close to the pick-ups and bridge. and it really gets in the way. other than that prs is awesome. gibson makes awesome pick-ups that is for sure. i have a duncun jazz and duncun classic set-up in a washburn idol 161. and i think its very good.
Also, check out Fralin and Lollar websites. These guys make pickups that are good for all styles. You can use your amp and pedals to dial in specific sounds for specific styles of music. In my opinion it is best to have a high quality set that is versatile instead of limiting yourself to a certain pickup that does only 1 thing well.
I just named several guitars I own. Some very nice . They all have a unique sound. Only you can decide which to use for what kind of music or sound you want. I will say though that I have severl Gibsons,Prs's , Epiphones . I f you are into box's , I like the Fulltone Catalyst for the Fender Strat. I haven't tried it on a Tele yet. You can really expand the Strat's horizons with this box. I love most all of my guitars for each of their contributions. Now, as for PRS. Well, I have two. A six hundred dollar GC bought (they will rip your wallet ). I really like playing it and a McCarty without birds. Very light and full of tonal possibilities. I use both Solid state and Tube amps. Man , I wish I could sell some of the guitars I don't use as much any more and pay of the credit cards. I'm hooked though.
You asked about pickups. Well My favorite will be the PRS P90's. Gibson's Burstbucker Pro's. The 57 ressiue fender strat.My G&L are very interesting (my newest axe). Well, have a good one .Jim.
I put together a guitar similar to the one backseatmemories is describing, with a JB in the bridge position and an Alnico II in the neck position, plus an Alnico II in the middle. (My JB splits to a single when I depress my tone 'switch'; but I rarely split it).
This setup gives the best of all worlds for me, because I need to be able to play all sorts of rock, from the 50's to the 90's. A humbucker in the bridge position is best for hard rock, punk rock, and even metal (not modern metal, mind you; you really should pair up active pickups, like EMG's, with an amp head and cab that are meant to handle that). And the single coils in the middle and neck position are best for blues, blues rock, 50's rock, 60's rock, country rock, etc.; whether they are only slightly distorted, or heavily distorted. Be advised, however, that 'classic' pickups really do sound best using vintage (or vintage modeling) amp heads and cabs ... seriously, it makes a big difference ... your friends will laugh at you if you try to play these through modern amps and cabs that are meant for modern metal ...
Anyway, I've had these pickups since the 80's, and have moved them from one guitar to another (I'm on the 4th guitar now) ... they are so versatile!
For really heavy metal, speed metal, nu metal, industrial, etc., definitely go for active pups ... you need the hotness to screech through everything else on stage.
If you're seriously into some of the more classic genres; then you ought to check some of these: For really great classic 50's and 60's rock (using older overdriven amps), the lipstick tube pups are cool ... cooler than you'd think from looking at the guitars they were in.
And for serious 60's blues rock, I opted for a config that has a P90 in the bridge AND in the neck position. What's really cool about P90's is that you still get the single coil bell-like chime from them; but, because they're much fatter than a typical single coil, when you over drive them, they sound fat and hot ... not exactly like a humbucker, but close enough to keep pace with a vintage humbucker ... from the perspective of the listening audience, that is.
Speaking of active pickups and modern heavy metal ... careful not to drop tune too low; the warp that you'll get in the vibration curve of the string will make your 4th and 5th strings sound like your amp is broken ...
One final word: match the pickups to the amp and cab ...
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