Autoconf and automake are horrible -- run, man, run fast away from them
Most projects which use them never really do it properly (because understanding how to do it properly is nigh impossible), and the configure scripts fail when you try to do something which is supposed to work out-of-the-box but was not expected and hence doesn't work (like using a cross-compiler).
Autoconf uses an obscure macro-processing language called 'm4', which in itself is quite neat, but here it adds an extra layer of complexity (and steepness of the learning curve) that really could have been avoided.
Scons is a better alternative (used by Doom3 code), we used that for a long time in a project and it got annoying after a while, it drives me crazy when the whole damn project has to be recompiled when I change a minor thing in a header file. Plus Scons is Python and that's when I discovered how much I hate whitespace-sensitive languages

Nowadays I just use normal Makefiles and I'm a lot happier.