The Nintendo Ghosts were/are Mario and Luigi. The once haunted the Acachalla's Household and Johnny Toast had to come to get them to leave. He successfully got Luigi to leave by beating him at Mario Kart, though they keep haunting the house.
During the balloon boy ragdoll episode, Johnny theorized that Nintendo would continue to send in game ghost to kill them for some unknown reason. It is theorized by some fans that it is because Spencer said Nintendo "isn't legit" and also saying "Valve is more legit than Nintendo." This may have angered Nintendo, and caused them to want to seek revenge against Spencer, thus sending more ghosts to the Acachalla household.