Is indeed a variation on Kung-Fu for the hacking community. It has been said that:

Kung-Fu means skill through dicipline,
Kung-Foo means skill through badass programming powers.

This term is rather flexable and can refer to pretty much any computer skills that you might posess.

The X-Files episode mentioned above is "Unusual Suspects" (episode: 5X01 which first aired 11/16/97) and refers to a scene in which Frohike of the lone gunmen demands to have his ego appeased by being told that his kung foo is the best before he will assist in hacking a government database.