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php_flag session.use_cookies off
php_flag track_vars off
php_value arg_separator.input ";&"
In your .htaccess files you can only change PHP_INI_ALL and PHP_INI_PERDIR type directives. For a list of those directives have a look at the table within the ini_set [php.net] documentation.
It is really useful indeed since it safes you from having to use ini_set [php.net] in all your scripts.
Using arg_separator.input to set the arguments separator to ; will save you from any hassle with non-escaped ampersands in query strings. So it should be present in all your root level .htaccess files or httpd.conf files.