Since upgrading to Leopard, I have noticed that iTunes refused to quit properly with anything short of a Force Quit. Instead, the dock icon remains in the 'hidden application' state.
After some digging, it turns out that the culprit for me was having iMote running. By quitting that, iTunes is finally allowed to quit completely.
[robg adds: The generic version of this hint would be to check any iTunes remote apps or other iTunes plug-ins if you're having troubles getting iTunes to quit.]
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