Wp admin – Set default value to 999 in comments

You can use

add_filter('edit_comments_per_page', 'return_999');
function return_999(){
    return 999;
}

since the user options are filtered in the WP_List_Table::get_items_per_page() class method :

/**
 * Get number of items to display on a single page
 *
 * @since 3.1.0
 * @access protected
 *
 * @return int
 */
function get_items_per_page( $option, $default = 20 ) {
        $per_page = (int) get_user_option( $option );
        if ( empty( $per_page ) || $per_page < 1 )
                $per_page = $default;

        return (int) apply_filters( $option, $per_page );
}

So you could do the same for edit_post_per_page and edit_page_per_page.

Or if you have other custom post types: edit_{CPT}_per_page.