A TARDIS Instruction Manual was, as the name suggested, a book that instructed in the piloting of a TARDIS. The Doctor's TARDIS had an instruction manual, but the Doctor rarely looked at it. When the Doctor did, he would disagree heavily with it, at one point even ripping out one of its pages. (DW: The Pirate Planet)
Tegan tried to understand the manual when she accidentally set the TARDIS in flight whilst trying to get herself of the Monarch's ship. She called it giberish and eventualy chucked it on the floor and stamped on it. (DW:Four To Doomsday)
Eventually, the Doctor took to using it as a doorstop. (DW: Vengeance on Varos)
During his seventh incarnation, one of the segments of the Key to Time took on the form of the TARDIS Instruction Manual that at the time belonged to his first incarnation. (DWM: Time & Time Again)
During his eight incarnation there was a quick star guid and the manual its self had it's own street in the TARDIS.(BFA:Orbis)
There was no information about an emergency stop in the manual. (DW: The Infinite Quest)
At some point, the Doctor disagreed with the manual so much that he threw it into a supernova. (DW: Amy's Choice)