Thanks for starting this thread. After being away from the hobby for so long, and having had most everything packed away until recently, I didn't realize how much "repair manual" material I had on hand.
The only repair manual title I can add that hasn't been mentioned previously is Ray L. Plummer's Toy Train Repair Made Easy--21 Lionel Postwar Projects published by Kalmbach/CTT in 2000.
I also have Peter Riddle's Greenberg's Wiring Your Lionel Layout, Intermediate Techniques published in 1993.