So I was changing some permissions on files in /usr/ and I did something stupid which led me to change permissions on a whole list of directories and reinstall KDE3.5. For the most part I have got my computer working again, however I have lost some icons (like for trash, or some files) and in general my kde start menu is not working. All the programs on the start menu fail to open. ( the computer continues as if they are going to open, but the windows never appear. I have tried "Presentation" "Network" "Internet Messenger" etc without luck, however GIMP did open.)

Does anyone know what I've forgotten to do, or why this would be happening?