Secret moves are something like cheats; they are moves that are intentionally put in the game by developers, but do not initially appear on early command listings. They are later discovered, or (more likely) revealed to publications.
For the most part, the commands are complicated and/or non-obvious, and are usually only intended to be flashy moves.
Sometimes, certain levels of super special moves fit this description for all characters; such is the case with the MAX2 supers from KOF 2002, for example.