Scripts and programs that we use at ICSI are almost all written in-house, by people like you. More often than not, they start off as quick hacks for special purposes, then gradually grow in usefulness and popularity, then have to get rewritten to clean them up and make them more general.
For the purposes of consistency and maintainability, we have tried to define conventions for scripts that are to be centrally installed. And because it's hard to predict a-priori which scripts are going to end up being widely used, it's worth at least considering these conventions for all your scripts.
David Johnson wrote a document of conventions for his so-called "Babylon Project" to standardize speech scripts. The original document along with some Perl modules is in /u/drspeech/src/babylon/ but here is a web-accessible version of his conventions document.
Of course the ultimate reference for how ICSI speech programs are written is the de-facto one of looking at existing programs. If you do this, you'll notice that many of David's conventions have not been put into practice. It's more a case of understanding what we were trying to achieve through the conventions, and striving to incorporate this spirit into your own programs.
[It would be nice to put something in here about the autoconf structure used by the make files for all the compiled programs that are distributed through the SPRACHcore source tree. Failing that, look at /u/drspeech/src/SPRACHcore and see what you can figure out!]
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