I use them when two bound values (like in a hash table) are not enough internally, but are enough externally. Then i create a nested class with the properties i need to store, and expose only a few of them through methods.
I think this makes sense, because if no one else is going to use it, why create an external class for it? It just doesn't make sense to.
As for one class per file, you can create partial classes with the partial keyword, which is what I usually do.