If you're a buyer:
It is becoming more common for the seller / seller's agent to charge a fee to the buyer for the seller's use of a short-sale negotiator. This person is supposed to be skilled in all aspects of the short-sale process and is supposed to take a lot of the routine tasks off the agent / seller.
However, unless your contract calls for you to pay for this service, you can refuse to pay it. Remember, anyone can ask you to pay miscellaneous fees, but it doesn't mean you have to submit to their request.
If you're a seller:
Using a skilled, competent short-sale negotiator will make life easier for both you and your agent. They will make the daily phone calls, faxes, emails, etc. and follow up on each of the mundane tasks associated with this archaic process. I usually see it costing about $400-$600 per transaction and either the buyer, seller or even the bank can pay the fee.