Negative work (in the physicists' sense of work) occurs whenever a force opposes a body's motion but the body still manages to move that way anyway (because of inertia or some other force).
So if I stand in front of a moving train, then when it hits me, I'm applying a small force to stop the train. But that is pretty small, and the train hardly slows down. I am having an affect on the train (however small), but as far as the quantity ‘work’ is concerned, I am doing negative work on it.
If Superman stands in front of the train instead, then even he is doing negative work on the train at first. But eventually the train slows down and stops, then starts moving backward. As soon as it starts moving in the same direction as Superman is pushing it, Superman is doing positive work on it.
Of course, the train is applying a force to me or Superman as well. In my case, the train is doing a positive amount of work on me, since I'm moving in the same direction as it's pushing me. On Superman, the train also does a positive amount of work at first, as it pushes Superman backwards. (Of course, Superman could stand still like a brick wall if he wanted to, but then he'd kill everybody on the train like a brick wall would, so he does have to move backwards for a bit as he slows the train down.) Then when Superman starts pushing the train backwards, the train is still pushing against Superman, but it's doing a negative amount of work since Superman is moving the other way.
You may notice that in all of these examples, the work done by the train on the person is opposite in sign to the work done by the person on the train. This will always happen if two objects are moving together. The forces that they produce on one another will be ‘equal and opposite reactions’ (that is the same absolute value but with opposite directions), while the distance moved will be the same (since they are moving together), and work is calculated as force times distance (with some business about vectors in there that don't matter to us since this is a one-dimensional example). So one will be positive and one will be negative, depending on which way the directions (of force and motion) match: positive for the same direction, but negative for opposite directions.
In this example, you can also understand work as a transfer of mechanical energy through direct contact; the train transfers energy to me, which sends me flying. Or it transfers energy to Superman until all of its kinetic energy is gone and it stops, after which Superman transfers energy to it as it starts moving again, only backwards. (Superman's motion is harder to calculate just in terms of kinetic energy, since he is also interacting with the ground and turning kinetic energy into heat through friction. So don't worry about that.)