Depends on the application, really. I'd probably go with Duncan Hot Rails for singles, and Gibson 57 Classics for humbuckers. I do have a Duncan Antiquity in one of my Les Paul's, and it's great, but I prefer potted pickups.
I'm quite partial to vintage spec Firebird pickups. I have a set of Duncan Antiquities in my Jaguar that I love, but I also love a Duncan SM-1N in the neck position of just about anything.
P90s are second for me. I have a set of BG "vintage" P90s in a Tele and they're fantastic.
The one I am playing. But the combination of pickups I am playing the most and having a ball with is combo of the Bryan Gunsher wound rock tele bridge pickup paired with his P-90 in the neck of my tele. Lots of fun to be had in that combination.
It always depends on the signal path and the sounds I'm trying to make, but my co#1s both have dimarzios right now - a pair of 36th anniv in my soloway and a model-designed dimarzio in my Sadowsky.
When I played mostly rock I used superstrats with Duncan JBs in the bridges and 59s in the neck (when I had a neck pickup).
i have Owen Duffy pickups in my strat......and they've been there since about 2002.....not gonna change them and would buy another set in a second, if i had a second strat.
Three pickups stand out for me, in my limited experience.
Fender Vintage Noiseless - I have been in love with the sound since getting the Deluxe Player's Strat. Gibson Classic 57's - I had them put into an Epiphone LP and it came alive. Lace Sensor Gold - I can't exactly put my finger on it, but I like them. I know they are supposed to have increased sustain, but there's something else there that eludes me when I try to describe them.