So far I haven't seen a comment that echos my thoughts. But I like both inline and EOF POD for two different purposes.
Inline works great when you are writing a module, you put some POD at the beginning and the end of the file, but it's nice to have the documentation for the methods right next to the code. This still produces a very usable perldoc page.
But for the end-user application (and I assume that this is either a shorter script or the glue script for a set of modules) I'd just put the whole POD either at the start or the end of the file since it is probably not necessary (or even desirable) to use POD to comment code.
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