The newest Magento Security Patch SUPEE-5994 has .sh extension and can be applied within command sh PATCH_SUPEE-5994_CE_1.6.0.0_v1-2015-05-15-04-34-46.sh
But if you don’t have ssh access to your Magento website you can use our github version of files which already patched for Magento version 1.6.0.0.-1.9.1.1. You can view & download patched files at this link.