I use qmake to generate the Makefile, and that works well. However, sometimes I want to add more stuff to the generated Makefile without having to edit the generated Makefil
This Qt blog post answers the question of QMAKE_EXTRA_COMPILERS and QMAKE_EXTRA_TARGETS quite definitively.
Very soon we will be introduced to QBS.. the new Qt Build Suite coming from Digia and the Qt community.. hopefully it is being really well thought out (and well documented, for that matter).