Since I teach first grade, I don’t feel too badly about prompting them to remember their manners–it’s part of the training process. So I may ask them, “Are you forgetting something?” when a thank you is in order. As they grow older, though, it gets more awkward.
There are also times when I think it is okay to expect and require certain niceties from students. Saying good morning is one of them. Saying thank you to the door holder is another one.
I like your idea of telling stories about good qualities. Calling attention to desirable traits does two things. It recognizes the student who did the deed, while also giving an example for others to follow.