Aside from MBSA which only focuses on MS patches, and secunia PSI (which I beleive is only targetted towards desktop / personal PC's), is there any other patch tool that can identify outdated/unsupported/unpatched software on windows servers, be it ms server app or other? I cant afford to pay for a pricey vuln scanner.

You can use System Center Configuration Manager, if you are looking for something different maybe you could try GFI LANguard, it's check vulnerability and patch MS OS and application as well as third party applications. Regards,