C: Running Unix configure file in Windows

Yes. If you stick to the standard C library, and POSIX functions, most is available on Windows. You may just have to find the implementations. There are implementations of things that do not require Cywgin or MinGW (such as a pthreads package, etc.)

Also, there is a great book that is written in the style of W. Richard Steven's Advanced Proramming in the UNIX Environment, and the book is Windows System Programming, author Johnson Hart. He has a 4th edition. It focuses on System Programming, there is no GUI treatment whatsoever.

http://www.amazon.com/Windows-Programming-Addison-Wesley-Microsoft-Technology/dp/0321657748

It is the best book I know of for a UNIX programming moving to Windows.

You can have a look at MinGW (and MSYS), which are similar to cygwin, but gcc produce native Windows executables. However, since the Unix emulation is not as good as cygwin, you may have to adjust your code.

Always try to following standarts even when porting applications. POSIX compliant compilers exist on windows/Linux. You can try mingw. It has full toolchain required to build standart POSIX application (GNU Linux as well). Check out Dev-Cpp it eases the work.