get_cfg_var() is an old PHP 3.0 era function, that returns the value for a directive in the php.ini file. This value may be valid or invalid, depending on whether it was overwritten by other configuration methods (e.g., httpd.conf or .htaccess). This function will always return the value that was typed in php.ini, if any.

ini_get() is a new PHP 4.0 function, that uses the new INI subsystem introduced in 4.0. It will always return the active value, and not necessarily the value that was in the php.ini. Generally, unless you're writing a script that actually deals with the php.ini file, you should always use this function and not get_cfg_var().