To purge the effects of Davros' computer virus, the First Movellan's systems rebooted. This allowed his true self, Mark Seven, to say a final goodbye to the Tenth Doctor before the reboot deleted his pre-Movellan memories forever. (AUDIO: The Triumph of Davros)
When his TARDIS lost power, (AUDIO: Last of the Romanovs) the First Doctor and Susan Foreman triggered a system reboot that restored the ship's systems. (AUDIO: For the Glory of Urth)
When the Dalek Empire invaded Gryphon's Reach, the Eleventh Doctor was able to turn the Krillitane rebels' biological cloaking device against the sensors of the casings. Receiving no sensory input, the invasion force was forced to reboot their armours, allowing the Doctor to get the rebels to safety. (PROSE: Father of the Daleks)