Seriously though, it's not impolite, it's just an awkward way to hold a stone.

And I will share the comment of one opponent who, when he disturbed the board position and I commented "You are far too strong to not know how to hold the stones" replied "I know, I just do this because it irritates people". I am confident he is the exception.

People who don't play go face-to-face over a board may not realize that there is a lot of body language involved. There is a Japanese word, tetsuki, for the way a stone is placed on the board. See this page on SL: http://senseis.xmp.net/?TeTsuki

Proper placement of go stones goes beyond the elegant two finger snap into place. It entails the entire process, which should be decisive, not rattling the stones in bowl, clicking them against the bowls side, turning them over on the table, but taking one and deliberately placing it in such a way that it only briefly and necessarily obscures the vision of the board and does not disturb the stones in place.

Topazg, yes; very annoying. (OTOH, even some top pros do it. )
Keep both your hands underneath your hamstrings between moves.

We are beyond bowing to your opponent...

Ah, sitting still patiently is a highly skilled art I think.

I have a friend who thinks there's an upside and a down side to yunzi stones. I like to play mine upside down just to irritate him

My friend got a nice floor board and good stones, and since I'm stronger than him I always play white. Since the white stones are clam shells and have the lines, I've taken to always playing with the lines up. It's been funny to see that become a distraction for him when he suddenly has to check all the white stones and see if I've been playing them that way all game.

Sadly, I'm a terrible fiddler with the stones whilst they're in the bowl person, making infuriating clicky rattling noises as I do it. It's a habit I really must break - it doesn't bug me when someone else does it, but I'm aware of how irritating it can be to some people.

I think ideally everyone should be able to handle sitting there, looking at the board, deciding when to move, and then picking up one stone out of their bowl and placing it on the board.

PS I also have a horrible habit of taking my next stone out of the bowl as soon as I've moved and sit there twiddling it in my fingers until it's my turn again.

PPS I think I must be quite an irritating OTB opponent in all honesty

Trust me, that's worse - I tried it and ended up rocking from side to side against my arms, some weird comfort distraction-prevention thing or something, I don't know. Generally I try to either sit there with my hands on my lap now, or slouch over with a thoughtful expression and my chin resting on one hand.

Ah, sitting still patiently is a highly skilled art I think.