There is a number of tools sitting on top of SCons, providing higher-level functionality similar to that of Autotools which are trying to make the developers life easier (e.g. WAF, SNOCS). Unfortunately, SCons itself has the major drawback - longer compilation time for the large projects.
I can recommend to try out SNOCS (which is a SCons reversed) for those of you looking for an easy dependency management and choosing compilation options in the single command (compiler, x86/x64, Debug/Release, static/shared libraries, test/install targets, etc.).
SNOCS also tries to tackle the long compilation time problem by storing the projects configuration output in the separate files, which allows the consequent builds to skip configuration phase altogether and go straight to the building phase (last feature is under construction now)
CMake's configuration becomes tedious in a larger solutions, so the build system maintenance takes a large fraction of the developer time. Luckily as Martijn already mentioned there is biicode which "uses CMake to generate your project with its dependencies".