During the retraction cycle of the undercarriage the rotation of the wheels is stopped to prevent gyroscopic rotational forces. When the brakes are applied it can cause any excess grease/dirt etc. to burn off as the brakes are absorbing quite a bit of energy, iplus the heat absorbed during taxi.
You can imagine the stress the brakes would be under in a rejected takeoff!
Actually, my understanding is that, while both of the above explanations are correct, the actual stuff you see is carbon- because they're carbon brakes, not steel anymore. When the system 'steps' on the brake pedal during retraction, the wheels stop pretty quickly, producing a puff of black carbon powder from the braking surfaces.
It only happens when a lot of brake power is used during taxi or when putting on the brakes before gear retraction.
It might also have to do with environmental conditions (if there's a lot of wind the stuff would probably disperse quickly so you don't see it for example).
AJ: I'm probably not very familiar with the subject, but I always thought that the stopping of the rotating wheels was to prevent further damage given a tire blowout during retraction inside the bay. Is that correct?