I am going to start off by saying that since Java 7 Update 51, that using self-signed certificates is pretty much a waste of time for Internet deployments. With Update 51, Oracle has beefed up the security aspects of Java, which now blocks self-signed JAR files from being run via the web – even for applications which only want to run within the restricted “Sandbox”.
There are a couple of ways around this. The first is to reduce your security settings from the recommended (and default) High option to Medium (in the Java Control Panel), which allows self-signed JAR files to be executed after presenting a scary warning message (for the time being anyway). When set to High you don’t even get a choice, it was just blocked. The second is to get your clients to import your self-signed root certificate into their trust store – this approach could work within a closed or corporate environment but won’t on the Internet. The third, and recommended approach, is to sign your JAR file with a code signing certificate which has been signed by a trusted CA, but this will set you back a few pennies.General CA Java OpenSSL