Those "wobbles" that you hear are called beats - they happen when you play two simultaneous notes that are very close in pitch, but not quite. As the two notes get closer together, the frequency of the beats slows down until both notes are the same.
(A quick search on google turned up
this page...)
I remember our psychoacoutsics lecturer in college telling us that that's what he used to tune his guitar - basically play 2 notes that should be the same, and fine-tune the offending string until the beats disappear.
Of course this method also will only tune the open strings together, so you'll still end up with the standard problems of being slightly out the further up you go. That said, I always thought that the reason you set the intonation was to stop this happening, no?