Make changes to MySQL global variables permanent across reboots

set-variable=var_name=value is the classic method to do this in my.cnf. Also, you can specify using flags as --set-variable=var_name=value. Earlier than MySQL 4.0.2, most configuration options were set using this method.

This is depreciated and even removed in MySQL 5.5. Most options can be set using their actual names in the my.cnf. If you need further help, please be more specific.

You just can add all the variables to /etc/mysql/conf.d/mysql.cnf file just after [mysqld].

[mysqld]
max_connections=1000
foo=bar

if you found [mysql] replace it with [mysqld]

To make a global system variable setting permanent, you should set it in an option file: http://dev.mysql.com/doc/refman/5.0/en/option-files.html