Main differences between registry and file_registry tables in Drupal SQL tables structure?
The file_registry stores entries for all uploaded files as attachments or file_entities to Drupal. Files marked for deletetion are removed at Cron and cleared from the table.

The registry table stores Drupal system information on all available code files available to the system from modules and themes. And more importantly includes all php classes used in the system and where they may be found. When you install or remove modules or themes from your Drupal installation php files are added/removed from the registry table.