This should be handled on a case by case basis, but if you are using the default MySQL table type of MyISAM (which is the default storage engine unless changed or specified differently) here are a few options:
The myisamchk utility can be run from a command line to check, repair, or optimize tables. It is normally run while the database is not running. For more information about myisamchk visit the MySQL website. Mysqlcheck is similar in function to myisamchk, but can be run while the database is running. For more information about
mysqlcheck visit the MySQL website.
If you login to the database, you can also run sql commands that might fix your problem. Examples:
mysql> optimize table your-tablename;
mysql> analyze table your-tablename;
mysql> repair table your-tablename;
For more information about table maintenance SQL visit the MySQL website. If you are getting MySQL error numbers and are not sure what they are from the command line you can use the perror utility to lookup errors. For more info on perror visit the MySQL website. Examples:
shell> perror 13 64
Error code 13: Permission denied
Error code 64: Machine is not on the network