I know exactly what you are talking about here. My son is turning 12 in just a couple of weeks and he starting "tic"-ing when he was about 3.
He began by humming - I mean ALL the time - with every single exhale of breath. When I made him stop he learned to whistle and whistled constantly. After that we had finger snapping, compulsive throat clearing, clicking his tongue, and by the time he was in second grade he was making a noise that sounded like a growl. (This one troubled his teachers! LOL!)
Every time we broke one habit, a new one began. He finally invented silent tics - nostril flaring, jaw jutting, toe tapping, face making, and the list goes on.
Both our doctor and the school counselor believe he has ADD and his doctor said that his tics harmless and may even be a healthy coping mechanism that allows him to stay more focused. (She said that kids with ADD can be natural multitaskers and may actually have a need to multitask in order to stay focused.)
If I force my son to stop one tic, he'll just replace it with another one that might be much worse, so I learned that I could teach my son a new tic to replace disruptive ones - chewing gum, wiggling his ears, making the shapes of piano chords with his hands (he is now an "air piano" expert) etc.
Basically, in my opinion, if the tic isn't a sign of a serious disorder and it isn't disruptive, let him keep it.