I've upgraded the Primate Labs Store to use Potion Factory's open-source Potion Store instead of my own collection of PHP scripts. While the PHP scripts worked, they were hacked together quickly back in February and lacked a lot of features that were already present in Potion Store.
It only took an afternoon to change Potion Store to suit my needs, in part because I've worked on Ruby on Rails projects before, but mostly because Potion Store is a well-designed application; jumping in and making changes is easy!
If you're an independent software developer and you're thinking of rolling your own software store, I highly recommend you take a look at Potion Store first.