You can use the complete gnu tool chain with eclipse.
All you need is a cross development kit for your target platform
and then add it to your eclipse workspace configuration or even as
default toolset.
An idea how to setup those tools can be found here for linux:
http://www.ailis.de/~k/archives/19-ARM-cross-compiling-howto.html
for windows you need to have the right sdk (for most systems the
standardsdk500 will do)
I never integrated the windows compilers in eclipse but it might work.
If your target system is an arm device with windows ce 6.0 and above I'd
write that part with visual studio.
I wish you good luck for your project.