Debian specific guides
The Debian library packaging guide: http://www.netfort.gr.jp/~dancer/column/libpkg-guide/libpkg-guide.html
How to deal with a missing .so extension when generating libraries with libtool: http://people.debian.org/~keybuk/libtool-missing_so.html
GNU Libtool and pass_all: http://people.debian.org/~keybuk/libtool-pass_all.html
GNU Libtool - Updating your Debian Package http://people.debian.org/~keybuk/libtool-updating.html
Escaping the Dependency Hell - A nice descrption of the hows and whys of the right way to do things from Steve Langasek http://www.debconf.org/debconf4/talks/dependency-hell/index.html
General guides, manuals and books that help alot
An online book on the GNU Autotools suite http://sources.redhat.com/autobook/
The Autoconf homepage http://www.gnu.org/software/autoconf/manual/autoconf-2.57/autoconf.html
The Automake homepage http://www.gnu.org/software/automake/
The Libtool homepage http://www.gnu.org/software/libtool/
The M4 homepage http://www.gnu.org/software/m4/