I too prefer Module::Starter
. Here at Yahoo! we have some special things we need to do to get the code on our distribution server; with Module::Starter, it was easy enough to subclass the base class (actually I subclassed Module::Starter::PBP) and add in our special hooks in Makefile.PL and templates for other files we need for our distribution stuff.
brian's Template Toolkit approach is way nicer as far as building files goes, and it might be a very fruitful idea for someone to try cross-pollinating Module::Starter and Template Toolkit to see if it would make it even easier to customize.
I think for most people either Module::Starter or Module::Starter::PBP will be good enough to get going. If you find there are things that you simply cannot deal with as far as what's assumed as the default, then customizing is easy enough to do that you can at least consider doing it.