I'm studying to be an electrical engineer, so I know a few things about this.
Between the brands? I don't really know-- DiMarzio's marketing stresses clarity, SD's marketing stresses warmth, and EMG's marketing stresses gain.
But, in the end, they all boil down to a couple of basic components.
1) A magnet (or magnets, in the case of a single-coil). These are made out of either an alloy or Aluminum-Nickle-Cobalt (aka "AlNiCo") or an iron-dense ceramic.
2) A bobbin made out of plastic or particle board
3) Copper wire
4) Steel pole pieces (in the case of humbuckers)
Ceramic magnets are stronger than almost any AlNiCo magnet, creating a stronger magnetic field, which means that the vibration of the string induces more current, which means stronger electric output.
More copper wire also enhances the magnetic field, but also acts as a resistor, which can limit the treble. If a pickup has more windings of copper wire, it will have a greater output, but will lose some presence.
Really, a decent set of pickups is equal parts science and alchemy-- certain things just seem to "work" for not-immediately-apparent reasons. Your best bet is simply to try out as many as you can (just make sure you are using similar strings, as they can have almost as much effect on overall tone).
Personally, the guitarist in my thrash band just got a set of TV Jones Filtertron-style pickups in his new axe, and they sound amazing through his Mesa Dual-Recto. When you have an amplifier with 6 cascading gain stages, high-output humbuckers, like DiMarzio Super Distortion and Seymour Duncan Invaders, not to mention most of EMG's lineup, become pretty redundant.