You are talking about two separate, but intertwined things here:
- Autotools
- GNU coding standards
Within autotools, you have several projects:
- Autoconf
- Automake
- Libtool
Lets look at each one individually.
Autoconf
Easily scan an existing tree to find its dependencies and create a configure script that will run under almost any kind of shell. The configure script allows the user to control the build behavior (i.e. --with-foo / --without-foo / --prefix / --sysconfdir / etc ..), as well as does checks to ensure that the system can compile the program.
Configure generates a config.h (from a template) which programs can include to work around portability issues. I.e., if HAVE_LIBPTHREAD is not defined, use forks instead.
I personally use autoconf on many projects. It usually takes people some time to get used to m4, however it does save time.
You can have makefiles inherit some of the values that configure finds without using automake.
Automake
By providing a short template that describes what programs will be built and what objects need to be linked to build them, Makefiles that adhere to GNU coding standards can automatically be created. This includes dependency handling and all of the required GNU targets.
Some people find this easier, I prefer to write my own makefiles.
Libtool
Libtool is a very cool tool for simplifying the building and installation of shared libraries on any Unix like system. Sometimes I use it, other times (especially when just building static link objects) I do it by hand.
There are other options too, see this question.
In short, you really should use some kind of portable build configuration system if you release your code to the masses. What you use is up to you. GNU software is known to build and run on almost anything, however you might not need to adhere to such (and sometimes extremely pedantic) standards.
If anything, I'd recommend giving autoconf a try if you're writing software for POSIX systems. If you need documentation and how-to links, update your question.
Edit
Don't fear m4 :) There is always the autoconf macro archive. Plenty of examples, or drop in checks .. write your own or use what's tested. Autoconf is far too often confused with Automake, they are two separate things.