I come from a background where I normally create one file per class. I organize common classes under directories as well. This practice is intuitive to me and it has been proven to be effective in C++, PHP, JavaSript, etc.

I am having trouble bringing this metaphor into Python: files are not just files anymore, but they are formal modules. It doesn't seem right to just have one class in a module --- most classes are useless by themselves. If I have a automobile.py and an Automobile class, it seems silly to always reference it as automobile.Automobile as well.

But, at the same time, it doesn't seem right to throw a ton of code into one file and call it a day. Obviously, a very complex application should have more than 5 files.

What is the correct---or pythonic---way? (Or if there is no correct way, what is your preferred way and why?) How much code should I be throwing in a Python module?

Think in terms of a "logical unit of packaging" -- which may be a single class, but more often will be a set of classes that closely cooperate. Classes (or module-level functions -- don't "do Java in Python" by always using static methods when module-level functions are also available as a choice!-) can be grouped based on this criterion. Basically, if most users of A also need B and vice versa, A and B should probably be in the same module; but if many users will only need one of them and not the other, then they should probably be in distinct modules (perhaps in the same package, i.e., directory with an __init__.py file in it).

The standard Python library, while far from perfect, tends to reflect (mostly) reasonably good practices -- so you can mostly learn from it by example. E.g., the threading module of course defines a Thread class... but it also holds the synchronization-primitive classes such as locks, events, conditions, and semaphores, and an exception-class that can be raised by threading operations (and a few more things). It's at the upper bound of reasonable size (800 lines including whitespace and docstrings), and some crucial thread-related functionality such as Queue has been placed in a separate module, nevertheless it's a good example of what maximum amount of functionality it still makes sense to pack into a single module.