Well.... a negative voltage in this case is just like any other voltage.
Its a difference in the potential of certain points.
Just as the difference between a +5 and ground is 5 volt... the difference between ground and - 5 is also 5.
If you switch polarity on the Volt meter(multimeter) you also get a negative voltage.
Its all in the reference points.
Well... the difference between +5 and -5 is 10volt so it can be used to get a lot of different voltages from just the 3.3, 5 and 12 volt lines.
And i can think that HD spindle motors use it for something but thats just a guess.