Digicert makes it pretty simple to get SSL certificates for Java web servers. I like.
They have a tool to generate the command line code you need to enter to generate your certificate request here:
https://www.digicert.com/easy-csr/keytool.htm
Just enter the appropriate information. Open a command prompt window on the server on which you intend to install the certificate. Navigate to the folder where you want to store the certificate files. Copy and paste the command into the command prompt window.
A file will be created for the keystore, and for the CSR (certificate request). Copy and paste the certificate request (in the .csr file that gets created) into the box on the order form where it asks for that information.
Once your certificate is approved, download and copy it to the folder you created above. Run the command on this page but replace the domain name with the domain name for which you ordered the certificate:
http://www.digicert.com/ssl-certificate-installation-java.htm