A while back I was introduced to a script which was used to download a given version of the Drupal core with a handful of modules AND copy any custom modules/profiles/themes under a given path inside the Drupal installation AND run the Drupal installation from shell! SO COOL! This completely eliminated the need to have 3rd party code in our repositories and it made (at least) my life a whole lot more worry free.
We are HUGE fans of simplicity, automation and open source. Here's one of our solutions for keeping track of Drupal module versions, custom/contrib code, deploying and taking backups. And more!