I've been creating SSL configurations for various groups in the company, and since I like the standard command line, I've been doing it via OpenSSL. However, some groups use Java-based SSL servers that need their .key and .cert in the Java Keystore format.
So to get the whole instruction set together in one place,
openssl genrsa -out servername.key 2048
openssl req -new -x509 -key servername.key -out servername.csr
#Send off the CSR to get it signed, and pull down the intermediate CA certificates that our internal authority uses to sign.
openssl pkcs12 -export -in servername.cert -certfile intermediate.cert -inkey servername.key > servername.p12
#Give it a password at least 6 characters long so that Java doesn't complain
keytool -importkeystore -srckeystore servername.p12 -destkeystore servername.jks -srcstoretype pkcs12