wewish.org doesn't work for me, although I don't get an Error 404, a Error 403 of no permissions to view the index page. EDIT: Fine for me too, now.
Generally files should be CHMODed to 644 or 664, and folders to 775 or 755. You use a FTP (File Transfer Protocol) application like FileZilla and right click one or a selection of folders or files and click Properties/CHMOD and change the value to 664 (for folders) or 775 or 755 (for files).
It will only change that particular folder only, and not the sub-folders and the files which reside in them to that same CHMOD.
I'm not sure what value of CHMOD will be accepted by GoDaddy, but you could certainly try either 644 or 664 for files and 775 or 755 for folders, and see if it affects if you can view files/folder directories.
I recently had Godaddy. They run their PHP as cgi so the files all need to be set to 644 and folders to 755. If you set either to anything higher than this you will have problems. For example, if you set a file to 775.... the server will not allow the file to be executed. All folders (including subfolders) need to be 755.
I really like hosts that run php as cgi though... better security.
On a side note, I also have in the past had just a few files that suddenly seemed to change their permissions... I don't know why.