Not liking the available options of CMake, Scons, or plain old Make, I decided to write my own utility.
Stir, best for small/medium projects (I imagine parts don't scale well yet), only needs to be told the directory structure of a project (or projects), it will automatically search for c/c++ sources files along with their dependencies (currently requires the compiler support the -MMD switch).
It's pretty new, but it's starting to be usable. If anyone could give it a try and some feedback, I'd appreciate it.
The doc.html file on the repository has the information on the configuration file format, and I've uploaded a Linux 64-bit binary to the repository as well as attached. It requires C++11 and 3 Boost libraries: filesystem, program_options, and system (they are statically linked to the binary in the repo).