GNU Autoconf, Automake and Libtool by Gary V. Vaughan, Ben Elliston, Tom Tromey and Ian Lance Taylor. Also known as "The Goat Book".
An Autotools Tutorial by A. Duret-Lutz. This is a great tutorial, but one of the nicest aspects of this web site is the list of Autotools resources at the bottom of the first page.
The AC Autoconf Macro Archive - an archive of drop-in components for autoconfiscated projects. Macros are fully classified for easy lookup, and full documentation for each macro is provided.