You can use the mysqlcheck command to perform several operations including check, repair and/or optimize.

example:
mysqlcheck -u root -p --auto-repair --check --optimize --all-databases
http://dev.mysql.com/doc/refman/5.0/en/mysqlcheck.html

Thanks Sonic84!

How to auto repair all databases with mysqlcheck

$ mysqlcheck -u root --auto-repair --all-databases

--auto-repair
If a checked table is corrupted, automatically fix it.
Repairing will be done after all tables have been
checked, if corrupted ones were found.

--all-databases
Check all the databases. This is the same as --databases
with all databases selected.

Thought I'd post these commands here, in case anyone needs to first do a full backup of MySQL, then check and repair all databases.

First command does a full backup of MySQL, this includes all databases, all GRANTs, etc.
Second command outputs a log so you can peruse table maintenance success, since Command Prompt on Windows doesn't seem to let you scroll up through the whole enchilada output.

mysqldump -u root -p<password> --all-databases > database_backup.sql

mysqlcheck -u root -p<password> --auto-repair --check --all-databases > database_backup.txt

removed -wrong posting

You can easily repair a database table using the DRS Softech MySQL Database Repair Tool in just a few simple steps:

1. 
   

   Download & Install the tool on your system.

   
   


2. 
   

   Launch the software and select the corrupted MySQL database.

   
   


3. 
   

   Click on Scan to analyze and repair the damaged tables.

   
   


4. 
   

   Preview the recoverable data before saving.

   
   


5. 
   

   Click on Save to restore the repaired tables.