The Autoconf system is compatable with Cygwin. I can imagine that getting a full autoconf system would be a project to remember.
I've used them before on Cygwin and PS2Linux and they're very convenient, but they take a while to run which tells me they'll take a lot longer to make. Personally, I'd settle for a GCC makefile, a Linux makefile, and of course the MSVC .dsp/.dsw files as an easy way of keeping everything seperate so stuff doesn't get mixed up. I have an old makefile (originally code.mak) that I've tried to bring up to date (mainly by changing all the file/folder names to lowercase) you might want to look at. I haven't gotten it to compile, but when it comes to editing makefiles I'm a novice. I also have no idea what changes have been made to the code since that makefile was made. (IIRC it was created from the .dsp file, which is something I'll have to look into now that I just remembered it, just have to try and remember the program name. Maybe, just maybe, running it on the new .dsp files will make a usable makefile.)
