Indexes make queries faster by reducing the amount of data that needs to be retrieved and processed. The three basic rules for designing good indexes are: 1) Retrieve less data by focusing indexes on columns used in WHERE clauses, especially equality comparisons; 2) Avoid point queries which require random access to retrieve each row individually; 3) Avoid sorting by using indexes to eliminate the need for operations like GROUP BY and ORDER BY. Composite indexes should place columns with equality comparisons first to minimize data retrieval.