I don't know how many people use Module::Build for more than bundling of code for CPAN. In fact I've been using it for years to help organize and build up my base of custom modules.

Typically this involves subclassing Module::Build and then adding a number of new features using its API. The documentation isn't terrible (but it could be better), but I'd still recommend looking at the code in Module::Build::Base whenever you are stuck trying to figure something out.

By default Module::Build only knows about a few directories. If you need to have files installed in any other directories than you can either modify the Build.PL file or you can add that information to a subclass and use it across all of your code. I'd recommend the latter. One particularly nice trick is to associate certain directories with XS (or other compiled code) and have Module::Build build it automatically for you.

Another nice thing about using a subclass of Module::Build is that now you can have a central source of file policy. i.e. a central location that dictates that certain files go here and that other types of files go there. Taking this out of the hands of each module is desirable for any project larger than a few modules.

Of the similar modules I have looked at Module::Build is the best. If nothing else it is much better than Makefile.PL.