Having used both autoconf and cmake, I have a strong preference for autoconf (plus hand written makefiles; never been able to get into automake). It's just easier to use for me, especially when it comes to writing tests for supported functions and adding optional features you want to enable or disable via configure script options.
In my opinion, automake is the weakest part of the autotools chain. Look at this section of the manual for example https://www.gnu.org/software/automake/manual/automake.html#G...: it says that automake doesn't recognize many Gnu Make extension, and can get confused even by weird whitespace...
