In essence the OS is the same, but interface differences and other mechanisms will require specific software. Your Pocket PC software will not run on Windows Mobile Smartphones. Windows Media files are ok, though.
It's a slimmed down version to be sure but with the more robust phone specific features (smart filter is my favorite!). They cannot use the same software as not only are the file structures different (and diff between 02/03) but a lot of apps have the display size programed so it fails there. That has been the biggest issue with companies who are trying to issue their own certificates using the old PDA cert apps.