Autotools is a build system for POSIX environments. It consists of a combination of tools: automake (http://en.wikipedia.org/wiki/Automake), autoconf (http://en.wikipedia.org/Autoconf), libtool (http://en.wikipedia.org/Libtool), GNU make (http://en.wikipedia.org/Make), intltool (http://freedesktop.org/wiki/Software_2fintltool), m4 (http://en.wikipedia.org/wiki/M4_%28computer_language%29), pkg-config (http://en.wikipedia.org/wiki/Pkg-config), gettext (http://en.wikipedia.org/wiki/Gettext), gcc (http://en.wikipedia.org/wiki/GNU_Compiler_Collection), perl (http://en.wikipedia.org/wiki/Perl), and others. Autotools is responsible for generating the configure (http://en.wikipedia.org/wiki/configure) scripts that many linux developers are familiar with.
There is a series of articles which walk through the process of creating an autotools project using Mono here:
http://wp.colliertech.org/cj/writing-free-software
For more information, see the wikipedia entry on the GNU build system (http://en.wikipedia.org/wiki/Autotools)