Do you remember Guile?
I'm a firm believer in adding extension languages to programs. As soon as a program is too complex to be run as a simple shell command (without too many command-line options) it needs at least a configuration file, and once you add that, the configuration options will start to get more and more complicated.
You don't want to write your own parser for such a configuration file. Ad hoc solutions will give you an awful format -- just think of sendmail -- and it really isn't worth the effort. A much better solution is to use an existing programming language and just embed it in your program.
That was the idea behind Guile. The inspiration was Emacs with its Lisp configuration and extension language. Guile is a Scheme interpreter and is designed to be easy to embed in your own programs.
To use it, you write a few handles into your application that can be called from Guile, then in your main program you initiate an interpreter, read the configuration file and let the interpreter evaluate it, and viola you have added a lot of flexibility to how your program can be configured.
For even more flexibility, you can read Scheme code interactively while your application runs, or you can define hooks in your configuration script that can be called by the application to customise it. I use both in CoaSim to get maximal flexibility in my simulator.
I don't use Guile any more. These days, I use Python for my extension language. Well, actually it is usually the other way around: I let Python be in charge and build packages that extends Python. I find Python easier to work with for most applications than I find Scheme, and there is no doubt that Python is much better known in the bioinformatics field than Scheme is.
Still, I fondly remember Guile. If you are interested in a little history lesson, check out A Brief History of Guile.