Well, I've just made a simple tool to scan up for empty folders and they really are a problem at least on my machine. Because I use Your Uninstaller for uninstalling it usually deletes all those logs, temp files and so on but leaves the folder there for some absolutely strange reason. Also, in case of iTunes, when it moves tracks from one folder to another it usually doesn't remove empty folders too. I can go on and on to list all possible ways where empty folders remain undeleted. And for those times when some app needs an empty folder to run properly a check box indicating whether to remove it or not would be great.