you should take a look at running a crosstool-ng setup on your windows box inside cygwin. and then have eclipse use that compiler. this will allow you to develop for your target linux platform easily.
here's some slides
it sounds like you're developing for a desktop/server platform, so you'll have to make sure you set up your crosstool-ng with the same versions of standard libs as your server has (libc, libstdc++, etc). you also want to make sure your crosstool-ng has the same version of gcc as the target as well.
if you don't want to mess with getting all that setup, you could always install linux as a virtual machine on your windows box and work inside there.
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