В httpd.conf в блок конфигурации каждого виртуального хоста добавляем:
  php_admin_flag engine on
  php_admin_flag expose_php off
  php_admin_flag safe_mode on
  php_admin_flag track_vars on
  php_admin_flag allow_url_fopen  off
  php_admin_flag magic_quotes_runtime on
  php_admin_value doc_root /home/user/htdocs
  php_admin_value open_basedir /home/user/htdocs
  php_admin_value safe_mode_exec_dir /home/user/bin
  php_admin_value safe_mode_protected_env_vars  LD_LIBRARY_PATH
  php_admin_value safe_mode_allowed_env_vars PHP_
  php_admin_value upload_tmp_dir /home/user/htdocs/tmp
  php_admin_value upload_max_filesize 1024000
  php_admin_value max_execution_time 10
  php_admin_value post_max_size  1M
  php_admin_value memory_limit 8M
  php_admin_flag mysql.allow_persistent  off
  php_admin_value mysql.max_links  5
  php_admin_flag pgsql.allow_persistent  off
  php_admin_value pgsql.max_links  5
  # в php.ini disable_functions =