With Windows Mobile 5.0, they're still two different platforms but with support for a common CAB structure - meaning you can package one CAB for use on both the Pocket PC and Smartphone. The mechanics behind a program for the Pocket PC and a program for the Smartphone are still different.
There's a short blurb on the common CAB structure in this article:
http://msdn.microsoft.com/mobility/d...atsnew_wm5.asp
I'm sure there's more detailed information hiding somewhere in MSDN.