the Challenger was NCC 71099 as a reference to the Challenger space shuttle, which was OV-099 (why the Challenger was OV-099 which was lower than the prototype OV-101 Enterprise i don't know)
began as a test vehicle (STA-099) then was later upgraded for spaceflight as OV-099. Incidentally, the early mockup/placeholder shuttle Pathfinder
was retroactively designated OV-098.
Kind of makes me wonder if there was a similar mockup NX-class ship that might have been designated NX-00.