Open Atrium 2 or Drupal Commons or Simple Drupal with OG
Drupal Commons has a terrible track record or maintainability and upgrade path.  I only recommend using Drupal Commons or Open Atrium when they fit your needs out-of-the-box.   If you have very custom needs, definitely go with a custom D7 &amp; OG build.

If you find that Drupal Commons or Open Atrium have features that you would like to replicate, then install them somewhere else and use them as a guide for creating your own features.  

The best answer is to say you need to try them all and determine their strengths and weaknesses according to your project, but from personal experience, I have regretted every project I've used Drupal Commons on, and won't do it again.

One project I did, we started with Drupal Commons, and eventually realized that it was not a good fit.  So we just copied all the features we wanted into a normal D7's sites/all/modules directory.