A stipend is an amount paid to someone for work completed. It is different from a traditional payment in that the amount is paid for a specific time period rather than on an hourly or annual basis. They're common in educational or internship situations, particularly Ph.Ds in the sciences.
An intern might receive a stipend, or set amount, for complete a three-month summer internship program. The pay is based on the time invested and not the work completed, according to About.com. Another example is a master's or doctoral student who receives a stipend for a research or teaching assistant position.