Here is a simple command to auto repair, check and optimize all the tables in all databases running on a MySQL server:
mysqlcheck -u root -p --auto-repair --check --optimize --all-databases
mysqlcheck is available in MySQL 3.23.38 and later.
mysqlcheck uses the SQL statements CHECK TABLE, REPAIR TABLE, ANALYZE TABLE, and OPTIMIZE TABLE in a convenient way for the user. It determines which statements to use for the operation you want to perform, and then sends the statements to the server to be executed. The exact operations are determined by the underlying storage engine used.
You must execute it on running database. It is recommended that you kill other incoming queries (like from your website) before running this which makes it a lot faster. I simply stop my httpd server before running it. You may want to use a Site Unavailable message instead so that the MySQL server is left alone.