A recently updated Apple knowledge base article suggests:
When iPod is connected to a computer there are times when it should not be disconnected by simply unplugging the USB cable. In these cases, iPod must first be ejected before it can be safely disconnected.
You may safely remove your iPod by simply unplugging the device if your iPod screen says, "Charging", "Ok to disconnect", the Main Menu is showing, or, if it is an iPod shuffle, the light is solid amber or solid green.
Be sure to eject
You must eject your iPod if you device says "Do not disconnect", "Connected, Eject Before Disconnecting", "Sync in Progress, Please Wait...", or, if it is an iPod shuffle, the light is a blinking amber.
To eject your iPod, simply select your iPod from the Device list in iTunes and press the eject button to the right of the iPod icon as shown below:
You can also eject your iPod from Finder. Simply launch a new Finder window and click the eject icon next to your iPod.