A TARDIS Instruction Manual was, as the name suggested, a book that instructed in the piloting of a TARDIS.
The Doctor's manual
The TARDIS Instruction Manual that belonged to the First Doctor was one of the segments of the Key to Time. (DWM: Time & Time Again)
The Doctor's TARDIS had an instruction manual, but the Doctor rarely looked at it. When the Fourth 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 while trying to get herself off of the Monarch's ship. She called it gibberish, eventually throwing it upon the floor and stamping on it. (DW: Four to Doomsday)
Eventually, the Sixth Doctor took to using the manual as a doorstop. (DW: Vengeance on Varos)
When an alien creature attempted to get into the TARDIS, the Seventh Doctor tried consulting the manual for help. However, the creature had already breached the ship's dimensional interfaces, which included time, and therefore it had already destroyed the manual even though it had not yet done so. (NA: Cat's Cradle: Time's Crucible)
The Eighth Doctor had a quick-start guide, while the manual itself had its own street in the TARDIS. (BFA: Orbis) Sarah Jane Smith had once happened upon a room in the Eighth Doctor's TARDIS where several thousand volumes of the TARDIS Instruction Manual were kept; she took this to mean the single book she had seen the Fourth Doctor use was just the introductory volume. (EDA: Interference - Book Two)
The Eleventh Doctor admitted that at some point, he'd disagreed with the manual so much that he threw it into a supernova. (DW: Amy's Choice)
Other information
- There was no information about an emergency stop in the manual. (DW: The Infinite Quest)