Trojans are viruses that has been presented as a "nice" thing. For example, the_best_blockbuster_film.mpg might actually contain a virus. They are known as trojans because it is named after the Trojan Horse, when the enemy built a horse filled with soldiers and present it to a castle. The castle accepted the horse thinking it was a gift and then got attacked when the horse was pulled into the castle.
For more information, see bots.