Another to look at is Bakefile.
Its main strength is taking a relatively simple input file (simple as XML gets, anyway) and putting out many different native build system files: Makefile.in on autoconf-based systems (Linux, OS X command line, BSD...), Visual C++ solution and project files, Xcode projects, MinGW and generic Unix Makefiles, etc.
That said, I don't know that I would use a system like this from the start. Since the initial target is Linux and the others are "maybes", consider starting with automake, and put the Bakefile (or whatever) move off until you do your porting. It's always a mistake to build things before you actually need them. There's always a tradeoff -- the Lowest Common Denominator Syndrome in this case -- and if you don't have to pay the penalty today, put it off until you do have to pay; you may never have to pay. If you go with automake and build your files sanely, the migration won't be too painful.
