If you're referring to files in /includes/modules vs files in /includes/templates ... then ... whereas the files in /includes/modules/ are used to extract data from the database, crunch numbers, do logic-processing, and prepare data to be sent for display; the files in /includes/templates/ are used simply to render the display of the data built by the modules.
Essentially it boils down to templates being used only for display, and modules being used for business logic and intelligence.