This is as much a survey question as anything: I would like to know what your favorite make system is and why. I have worked with a number of them over the years though in recent history I have been leaning more towards those that work in cross-platform environments.
My "go-to" make system is CMake CMake - Cross Platform Make
Pros: Easy for new programmers to grasp, works remarkably well across Win/Lin/Mac, well documented.
Cons: Not as well known.
Second choice is SCons. Written in Python (a language I know), works well on non-standard platforms. Cons: I cannot name anything specific but have had issues with it in the past with dealing with loadable libraries (DLL on Windows, Shared objects on Linux).
I have worked with autoconf/automake in the past and can generally get the job done but it has one heck of a learning curve (compared to the others).
Bakefiles: when doing a wxWindows app this is pretty much the defacto standard for building and since it is just XML, it is easy to work with. Works well on Win/Lin/Mac. Cons are that it is not that well known or documented.
How about you?