We are looking for adequate build tool for a desktop GUI application to be written in D (using Qt toolkit), consisting of several native libraries, using 3rd party C-lib(s). It
I've seen CMake used in many more places than Waf. Most importantly the KDE project is now using CMake.
I did some research on google code search:
there are 2,097 wscript files in various opensource projects
compared to 36,914 CMakeLists.txt.
So CMake is definitely more popular.
I also tried to use google trends to see which was gaining more traction CMake or Waf. I wasn't succesful as Waf is too general at term (ie Wife Acceptance Factor), and "Waf build" doesn't show up in google trends at all.
Scons is known to have terrible performance issues. As Waf is a Scons derived I worry about its performance.
Lastly, CMake has terrible syntax and Waf has beautiful syntax. Since you're going with D it looks like you're willing to go off the beaten path for superior tools. In that case Waf may be the perfect fit.
Waf is very fast and has been chosen as the build system for Samba (http://samba.org/). It is also used by many proprietary projects because it lets you do crazy things that are impossible in Make/CMake.