The Dock
Nearly as bad as rebooting the user's computer is the bad habit of adding items to a user's dock. The only way to do this is by restarting the Dock and changing the preferences underneath it. Never do this. When you restart the Dock, you restart the Dashboard. Most users will not appreciate this. In addition, if the user wants your application in their Dock, they will put it there. Leave the choice up to the user.
Apple is probably the biggest offender in this area. I have also noticed a few third-party installers that give you this ability.