I'd like to see a feature that removes files from the shared files list after checking if the file is still there. Maybe the function could be locked for the incoming folder - i'm not sure if checking manual added dirs will be necessary or even useful.
The main idea is to stop aMule telling me that file xy isn't there if i removed it from the incoming folder after completion. Normally the file will still be in the share list, so that other people still try to download it. If that happens, aMule adds a log message "file xy not fond", but it still tries to share it. So if you don't remove the file from the list manually (reload button) the log will grow rapidly (depending on the popularity of your up/download).
A simple solution could be to remove the file from the share list after checking if it's really there or not. Another addition could be to check the permissions on files that are manually added (share a complete dir...) if the upload fails. I did not test it, but if aMule doesn't have the permission to read a file or to enter a dir inside the shared dir it should also give the "file xy not found." message.