With Linux you are never on you own and you are never dependent on one single entity to provide permissions. There are many support options and you have the freedom to choose your support options for any part of the system through many competing sources.
With Windows CE you must adhere to the license and restrictions as set forth in the complex license agreements that must be agreed to. Get a lawyer. With windows CE you have only one proprietary source for OS support and you will proceed only as they see fit to support and provide what you need. You may not agree with their position, but will not have any recourse but to bend to what they prescribe. The costs of incremental components, modules, development kits, licensing, and support tend to pile up with proprietary platforms. In the longer term, what happens when the vendor no longer desires to support the platform and you do not have the rights to support and distribute it yourself? What happens when the vendor moves to newer technology and wants you to move along with them even though you may not be ready to make the move? $$$
Our experience with Windows solutions in general is that they tend to become more expensive over time. What was originally considered lowest TCO gravitates quickly towards and solution that is encumbered and costly to maintain and support. Licenses have to be re-negotiated over time and the new technologies, often unneeded, are forced into the picture at the whim of the provider for the sake of THEIR business needs. On top of that, the license agreements are CONTINUALLY changing--get a lawyer.
With Linux you have the freedom to provide in-house support and expertise without being encumbered against distributing the solution as you need. You also have the freedom to continue to use and support technology that original providers no longer want to support. Having the source code and the RIGHTs to do with it what you want (GPL, LGPL) is a powerful attractor when it comes to business continuity and containing costs while providing access to the very latest technologies or technologies that fit your needs.
