It doesn't stand for anything. X is added to make the name sound better. Megaman X, Sonic X, etcetera. It could stand for Extreme or something but that's looking a bit too much into it.
The X is not an abbreviation of another word. X-Radiation is a form of electromagnetic Radiation having a wavelength of 0.01 to 10 nometers. In other languages XRays may be called Rontgen Radiation...