If you are thinking about a robotic joint as power comes into the motor and causes the link to move, then you're missing part of the picture. I say this because in some ways you could then imagine a negative torque meaning that something pushes on the link and provides power back to the motor.
The reality is that each actuator must be given an axis about which to rotate. Rotation in one direction is given a positive meaning - for example, maybe the encoder counts up when the link moves in a counterclockwise direction. A positive torque would be required to move the link about the axis in that direction, and would result in a positive velocity. The positive torque is provided by commanding the motor to spin its shaft in a certain direction.
A negative velocity is simply a motion of that same link, but in the opposite direction. In the example above, it would be a clockwise speed about the axis. The motor must exert a negative torque to cause this motion. In other words, it must be commanded to rotate in the other direction.
It's that simple.