I opened up this can of worms over on the IO forum... :) Everyone there said it was a bad idea too, but I didn't believe them, so I kept looking. Well, it is a bad idea...
You can only get CE (AFAIK) as part of the MSDN.. I have CE x86 dev platform as part of the MS Universal Subscription. I read all the SDK docs and went over MS's online documentation, and what it comes down to is installing CE on the IO or whatever is only as difficult as building a distribution on a CD and loading it. The problem comes when you want anything else to work, like video, sound, or USB. MS provides "driver templates" for all of these things, but you need to write device-specific drivers to make it work. Given that, as others pointed out, MS abandoned CE the chances of finding any of this pre-written is next to none. Which means a lot of work that will ultimately get you little more than a slow, underpowered OS that is compatible with nothing.
There are better options out there... Personally, I run Windows 'cause the apps I like and am familiar with run on Windows - I had stability problems with 98SE but 95B/USB works great (streaming MP3s off the CD-ROM on my TV right now.. :). But Linux or QNX or even Be x85 are very good small-footprint options. Hey, you could be the first person running Solaris x86 or NeXT x86! :)