Details were released yesterday of a very close call with Atlantis during the STS-27 mission with 5 time shuttle astronaut Hoot Gibson. This was a secret military flight, so not much has been said about it until now. It was also only the second flight after the Challenger disaster in 1986.
During launch, a chunk of debris came off the top of the right booster and bounced all the way down the right wing of the shuttle damaging about 700 tiles including blasting away tiles down to the bare aluminum. Astronauts looked at the damage with the camera using the robot arm. Seeing how bad it was, Hoot Gibson pretty much figured "we are all dead". During reentry, Gibson monitored control surfaces for any indication of failure of the wing and figured if he saw some deflection, he had about 60 seconds left to live and would use that time to tell mission control how he really felt about their diagnosis of he problem. Ground engineers basically blew it off and said "things will be fine, don't worry about it". (See the white spots on the shuttle wing in the photo)
Mike Mullane wrote a chapter in his book "Riding Rockets" which was quite scary to read. Read the book if you haven't it's one of my favorites up there with Mike Collins' "Carrying the Fire" - which is probably the finest books written by an astronaut.