Under Windows, to configure an Oracle instance to start automatically when its service starts, make sure that the following registry key is set:
HKEY_LOCAL_MACHINE\SOFTWARE\ORACLE\HOMEID\ORA_INSTANCE_AUTOSTART=TRUE
where ID is the identification number of the Oracle home (typically '0') and INSTANCE is the name of the instance. The corresponding service will be named 'OracleServiceINSTANCE'.
Also note that it is generally a bad idea to stop and Oracle instance by simply stopping the service.