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My scenario, is allowing a java application to call an https address on another computer that has a self-signed certificate. By default the jre will not accept self-signed certificates.

The paths will be slightly different on Linux.

You'll need to know the following paths:

• The path to the certificate file. Usually named something like server.cert
• The path to the jre that you are using. Be aware that you might have more than one jre installed on your machine. You need to use the jre that is being used by the java program that is consuming the certificate.
  In my case, that path is:
  C:\Program Files (x86)\Java\jdk1.6.0_13\jre\

Once you've figured out the above, you can:

• Start a SuperUser/Administrator console by going to the start menu and right-clicking on the "Command Prompt" program. Select "Run as Administrator".
• Import the certificate
  "C:\Program Files (x86)\Java\jdk1.6.0_13\jre\bin\keytool" -import -file C:\enterThePathToTheCertificateHere\server.cert -keypass changeit -keystore "C:\Program Files (x86)\Java\jdk1.6.0_13\jre\lib\security\cacerts" -alias servername
  Enter the password "changeit" (yes it really is "changeit")