For my first few distributions, I used h2xs. Eventually I grew tired of having to make a dozen adjustments to the generated stubs before getting to work.

So I created a template distribution, and would svn export it as needed.

But now I have my own script to create my stub distributions. It's called mkdist and is bundled with Module::Package::RDF. It's not especially configurable though - if you don't want to build your distributions exactly the same as I do, then you're out of luck.