I just finished a project that included a MySQL option in the installer and I wanted to let you all in on the secret. I used NSIS, so these were mostly ExecWait commands but here's the command prompt versions:
;run the installer
msiexec /i "MySQL_Setup.msi" /quiet INSTALLDIR="D:\Program Files\MySQL\MySQL Server 5.0"
;here you can dump a my.ini file in the same directory like I did
;install the service with your settings
D:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld-nt" --install MySQL --defaults-file="D:\Program Files\MySQL\MySQL Server 5.0\my.ini"
;change the password (if you want to). Make this the only line of C:\mysql-init.txt:
SET PASSWORD FOR 'root'@'localhost' = PASSWORD('mypassword');
;set the password to change at the next start
D:\Program Files\MySQL\MySQL Server 5.0\bin\mysqld-nt" --init-file="C:\mysql-init.txt"
;start the service
net start MySQL
Hope that helps!!!!