Well, the Boeing 737 (at least the fuselage) would be a good choice:
Boeing 737 flat car load #1
Boeing 737 flat car load #2
Boeing 737 flat car load #3
Boeing 737 flat car load #4
These are all Next Generation (-700/800/900) aircraft, the older (-300/400/500) were shipped in two pieces.
Also, I can't find the link right now, but I know there's a picture of a P-8 Poseidon fuselage being shipped this way as well (similar to the -800 fuselage, just different windows/doors).
Edit: Just found this page.
(The Oddball 707 would be an excellent choice for a starting point for these!)
Also, the 757 cockpit assemblies were shipped by rail as well (have a picture... somewhere.
The Santa Fe Railway operated some DC-4 aircraft under the "
Santa Fe Skyways" name (until federal regulators forced them to quit in 1947).