In the Console click on Settings, then click Shutdown, and you will be prompted for either shutdown or restart, this image shows it nicely:
http://mswhs.files.wordpress.com/2010/02/howtogeekshutdownorrestart.png
If a USB drive is part of your storage pool, then you must go to the Server Storage Tab, select the drive, right click, and select remove, at which point it will copy all of the data off that drive onto another drive available in your storage pool.
Once all of the data is off the drive then you can remove it.
If the drive isn't part of your storage pool at all, then I guess you have the choice of either unplugging the USB cable, or shutting down the server, then removing the drive.
Personally I always shutdown the server, then remove the USB drive, but that's because they were always part of my storage pool, then restart the server.