Deleting modules from the database that aren't on the filesystem
Try the Schema module.

This module compares the live database structure with the schema structure declared by all enabled modules, reporting
on any missing or incorrect tables


  The Schema module provides additional Schema-related functionality not provided by the core Schema API that is useful for module developers. Currently, this includes:
  
  
  Schema documentation: hyperlinked display of the schema's embedded    documentation explaining what each table and field is for.
  Schema structure generation: the module examines the live database    and creates Schema API data structures for all tables that match the
  live database.
  Schema comparison: the module compares the live database structure    with the schema structure declared by all enabled modules, reporting
  on any missing or incorrect tables.