Identifying Community Modules vs. Custom Modules
I am unaware of any full list of modules that are on drupal.org for public consumption (there are a lot).  If I were you, I would do one of two approaches.

Based on https://stackoverflow.com/questions/6136022

cd sites/all/modules
for module in *; do
  echo -n $module
  echo -n ': '
  wget --spider --no-check-certificate -S "https://drupal.org/project/$module" 2&gt;&amp;1 | grep "HTTP/" | awk '{print $2}'
done


Lines that print out with a 200 exists; ones that don't should give a 404.

The other option is  

cd sites/all/modules
for module in *; do
  grep 'project = ' $i/$i.info
done


Only modules on drupal.org will have a project line, which gets added by the packager script.

Also, if you visit the Available Updates page (admin/reports/updates) and check for updates, only public modules will be listed.