Should you be at a bus stop where multiple busses stop, and a bus begins to approach, but it's not the bus you plan on taking, it's courteous to shake your head 'no' at the bus driver, so he no longer has to waste time stopping for someone who will not get on. The next tip, however, is of even more importance:

Do not make any sort of signal to a bus driver you want to stop for you (other than maybe taking your bus pass out) Don't wave your hand or make any gesture. My girlfriend once did this, and the bus driver took it as a signal to pass us by. Oops.
The above (maybe) works in the US. In Mexico you vigorously wave your hand (and newspaper, if you have one) to stop a pesero.
Since the pesero driver is a very private entrepreneur he might well elect not to pick you up, maybe because he is in hurry, or because you look like a bad guy.

Government buses, on the other hand, stop no matter what.
What is difficult is getting them to move.

I doubt there is really any standardization for bus driver/passenger intercommunication, but this is what I've observed of the protocol in place:

When a bus is coming which is not the one you want to get on, step back from the curb. There doesn't seem to be any sort of hand signal necessary to inform the driver that you don't want it to stop.

When the bus you want to get on is coming, move towards the curb or side of the street (but not close enough to put you in the path of oncoming traffic or anything) and hold your hand up. Do this when the bus is still at a distance at which it can safely stop where it needs to.

It's just as important to properly signal the driver from within the bus when you want it to stop. Try to ring the bell just after the bus passes the stop before the one you want to get off at, or one block before, whichever distance is shorter. Don't ring it more than once, or the fnords will eat you. If the bell is not working right, call out "Next stop, please".

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