A pretty good Autotools tutorial (presentation/PDF) that already tells you more than you would like to know (which, alas, is probably less than you need to know).
Ars Technica describes it as
Autotools, an intractably arcane and grotesquely anachronistic cesspool of ineffable complexity that makes even seasoned programmers nauseous.
2008-04-01: Found these:
Stop the autoconf insanity! Why we need a new build system.
What is Wrong with Make?
Make alternatives: “SCons is my preferred tool in this category and also my preferred build tool overall.”
It was (is) a fundamentally misguided idea to make up a new limited language for use with make, then another one for automake, and another for autoconf. Who has heard of m4, really? And tools that add an extra script (and sometimes a language!) for creating the input to this vicious chain are even worse. One of the useful lessons from the Lisp people is that is really easier, and better, to use a real language than to make up and parse and understand a limited one.
The sooner everyone moves away from the make/automake/autoconf madness the better.
SCons is written in Python, uses real Python for its files, and might be the future. Or it might suck. It’s too early to tell; it has only been around for a decade or so.