I always use an open- or closed-hand to stop the clock.  I believe it's an important signal to communicate with the timer.  I know it has been discussed previously on this board that it isn't necessary on certain calls (ie jump-balls) but I do it because that's what I've been taught at camps.  I pay those guys a lot of money to teach me good techniques so I am going to follow it.  They also assign me games too 
-Josh