SSL Cert providers such as GoDaddy and RapidSSL claim 99% recognition -- what happens in the 1% non-recognition, and what is recognition, exactly? Should I just self-sign my certificate, instead of buying one? Is there such a thing as 100% recognition?
Recognition is dependent on the Certificate Authority that issued the certificate and if the browser recognizes the Certificate Authority.
Trusting the SSL Certificate
Browsers determine whether or not to trust an SSL certificate by checking the source of the certificate issuance. If the SSL certificate is issued by a Certificate Authority that is known and trusted by the browser, the browser extends that trust to the web site secured by the SSL certificate. If the certificate is self-signed or issued by an unknown Certificate Authority, the browser may display an alert or security warning.
Root Certificate Ubiquity
Most browser vendors release their software with pre-installed root certificates from known Certificate Authorities. An SSL certificate's root ubiquity or level of browser recognition (also called browser compatibility) reflects the number of browsers that trust the Certificate Authority. There may be a few older or uncommon browsers missing root certificates. This is why SSL providers do not claim 100% browser compatibility.
http://www.rapidssl.com/learn-ssl/ssl-browser-compatibility/index.html
If you have a self-signed certificate, you'll get 0% recognition since nobody will recognize you as a valid certificate authority. When a certificate is invalid, the user will get a very ugly warning and, depending on the browser, be told not to accept the certificate and they won't see your site.