Windows CE is a nightmare on low power modern embedded processor boards, embedded Linux is the best way forward, you can use ncurses for console type apps, or if you want something quite powerful use a lightweight version of X and use SDL (Simple Directmedia Layer). That's only if you want graphics, I personally use an Ubuntu version with the same Kernel as the embedded OS, such as 2.4 / 2.6 / 2.8 etc, and find that the toolchain works fine. Plus embedded Linux is free, unlike CE which needs licensing, and the BSP (Board Support Packages) are not being updated properly in my experience (newer DM&P VDX/VSX x86 specifically).
I do a lot of embedded systems, most routers are embedded systems, and all run a variant of Linux (or more specifically, NOT WINDOWS CE!).
You can even use Java VM on embedded Linux, so you could use the 2D/3D canvas routines built in if you really need to, maybe if you have a big enough flash disk, use something like QT ( didn't they do a QT Embedded?)
Hope this helps!
Cheers,
Wilksey