Autotools is a build system for POSIX environments. It consists of a combination of tools: automake, autoconf, libtool, GNU make, intltool, m4, pkg-config, gettext, gcc, perl, and others. Autotools is responsible for generating the 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:
For more information, see the wikipedia entry on the GNU build system