What happens is that when a directory hierarchy is "deleted" in nautilus (or any other application that uses the method explained by Martin in comment 16), it gets moved to the $trash/files directory, and then when the trash gets emptied, that hierarchy is moved to the $trash/expunged directory, after which it should be deleted. Unfortunately, deleting all those files is not always possible when somewhere down the tree there are files or directories with permissions that don't allow them to be deleted by the desktop user, and then those files remain there forever, without any warning for the user...
What happens is that when a directory hierarchy is "deleted" in nautilus (or any other application that uses the method explained by Martin in comment 16), it gets moved to the $trash/files directory, and then when the trash gets emptied, that hierarchy is moved to the $trash/expunged directory, after which it should be deleted. Unfortunately, deleting all those files is not always possible when somewhere down the tree there are files or directories with permissions that don't allow them to be deleted by the desktop user, and then those files remain there forever, without any warning for the user...