The process mysqld reads the file my.cnf to load startup options for the MySQL Server Instance. The corresponding file for Windows is my.ini.
Groups are created within my.cnf to specify options for different mysql client programs and utilities. Such groups include:
[mysqld] [mysqld_safe] [mysqldump] [myisamchk] [mysql]
Multiple my.cnf files can be used. One for the server, one for utility programs (mysqlchk, mysqldump, mysqladmin, etc.) and one for the mysql client for setting session values and password.
Example: Login using mysql client with a my.cnf that specifies that binary logging is disabled for your command line session (sql_log_bin=0) and you have the SUPER privilege.