This is a FAQ on almost every Pocket PC and/or Windows CE development site and forum. This time I found the question on www.pocketpcdn.com.
Windows CE (.NET if a 4.x version, version 5.0 loses the .NET and is just Windows CE again) is a collection of pieces of an operating system, referred to as components. Each component is identified as belonging to Windows CE of a particular version and many of them are specifically written for Windows CE. An OEM, another third-party, or Microsoft themselves, can define a platform - a specific selection of those components to run on a particular device or compatible devices. A platform is a specialisation of the general set of components. Some of the components build on top of each other, others are completely independent, and others are mutually exclusive (e.g. you can only have one of the COM or DCOM runtimes).
Pocket PC is a platform defined by Microsoft; the 2000 and 2002 versions are based (loosely!) on Windows CE 3.0 while the 2003 versions are based on CE 4.2. Any OEM willing to license the software platform from Microsoft can do so, but must satisfy certain constraints (I believe) on screen size, application keys, and third-party components.
The tool for building your own platform comes in the Windows CE box and is called Platform Builder. You can find some videos demonstrating Platform Builder for Windows CE 5.0 at Channel 9. CE 5.0 will be released soon with a new Pocket PC version to follow later in the year, we believe. Once you've designed, built, and shipped your platform, you can generate an SDK from Platform Builder for use with (currently) eVC 4.0. A platform build consists of both compiling some components from source and linking other binaries together from supplied object libraries.
So, while Pocket PC includes many Windows CE components, some components of Pocket PC - notably the shell and messaging applications - are only available on that platform. It's possible to write programs which are source-compatible between Pocket PC and other Windows CE-based platforms, and even binary compatible, if you stick to components which are available on both platforms. So I guess the answer is really yes and no.