It sounds like what need is to have your programs digitally signed (i.e. Code Signing). This is similar in concept to an SSL certificate, in that it proves that the program is from whomever the certificate was issued to & has not been modified (e.g. malicious code added).
The thing key difference to understanding Code Signing though, is that the certificates are seperate from SSL certificates - they're specifically called code signing certificatescode signing certificates
.
I've used VeriSign in the past when going through the Microsoft Logo Certification programMicrosoft Logo Certification program, but found that their certificates are much more expensive than those available from GoDaddy or Comodo.
Edit
Also, there's an article on MSDN: Introduction to Code Signing that you may find useful too.