While many players simply use the wah pedal to 'wah' or 'quack', others take things a lot further:
Frank Zappa used wah pedals extensively, but not always in the conventional manner of simply rocking it back and forth - he often left it set in different positions to produce specific tones. Indeed, many other players such as Vai and Satriani have realised that they can use wah as a very powerful tone control - after all, it has the ability to boost a narrow range of frequencies to a far greater degree than any such controls found on guitar amplifiers.
The wah pedal can be used to great effect in hunting for resonant frequencies when playing at volume. By slowly moving the pedal, one can 'tune in' to specific harmonics, thereby encouraging feedback. Joe Satriani for one uses this to great effect.
Virtually any un-pitched noise created by the guitar, such as string damping and body striking, can be modulated by wah, giving it an almost drum-like quality. String scrapes work particularly well too!