Alexandre Duret-Lutz’s tutorial is my resource of choice.
There are also:
- Autotools: a practitioner’s guide to Autoconf, Automake and Libtool
- Autotools Mythbuster
To me, the autobook is not up to date anymore and more difficult to read. However it still contains interesting chapters like Writing Portable Bourne Shell.
Also, consider learning about non-recursive automake which addresses the concerns raised by Peter Miller in his Recursive Make Considered Harmful article.
EDIT: for reference, there is also Autotools Tutorial for Beginners.