Check Heavy UI
This module unobtrusively adds additional checkboxes to the permissions form located at admin/user/permissions - the additional checkboxes provide a much friendlier interface for dealing with the hundreds of checkboxes that accumulate on the permissions page as roles and modules are added to a Drupal installation.
On a test Drupal site I set up with 6 user roles, 105 core and add-on modules enabled, 9 content types, and the content permissions module enabled, there were 138 distinct permissions and 828 individual checkboxes on the permissions page. To initially set up the permissions to something sane, it took me about 17 minutes. On my first attempt of using this module after fully developing it, after wiping and restoring the database from a back up, it took me around 5 minutes to set up the same permissions. The point is that this module will save you time, especially on large sites.