This is the most common project format on Linux. It has been designed to distribute source code packages on a wide range of Unix-like systems. If you have ever installed a program using configure, make and make install, you probably have already used it as a user.
It is typically a bit more difficult to use as a developer. However, it is the default backend for Anjuta, which has features that make it easier to use. All the project manager's features are enabled when using it. You should be able to maintain a project using the Autotools backend without writing a line in configure.ac or any Makefile.am files.
Autotools files give more information than a makefile, but the backend does not support all the possible tricks. If you find a project that cannot be read correctly, filing a bug report will be appreciated. In the meantime, as a workaround, you can use the directory project backend instead. It is much more limited but should find all source files.
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