A good deed is what the school master used to tell if a soul was good or bad. The deeds had to be born from the soul which is why Sophie's didn't count. When one used them to do manipulate something, it counted as a bad deed. It is shown in the beginning of the book, that Sophie did many "good" deeds in order to get into the School for Good. The deeds were often stuck up and shallow ike when she gave soap and mirrors for her "good deeds".