For classes/roles/utility packages, I will normally include pod at the end of the pm file. It just seems neater to have it all together, and the most logical order for methods to be documented in isn't always the same as the most logical order for them to be programmed in.

As an exception, for a handful of projects parts of the code, tests, and/or documentation are auto-generated based on templates, and in those cases I'll often want to generate the documentation, code, and tests in separate files for convenience.

Some documentation is more overarching and tutorial-like in nature, so lives in separate pod files.