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You can create a Java Keystore and save it as a file (that is easiest and is cross platform and is what I would recommend if it works for you).
You can access Windows Secure Cryptographic Storage using VBScript (in IE) embedded in the page (not really recommended...) or by calling out to a native library shipped with your code (http://msdn.microsoft.com/en-us/library/aa380256%28v=vs.85%29.aspx).
You can access the Mac OS X KeyChain by calling out to a native library shipped with your code (http://en.wikipedia.org/wiki/Keychain_%28Mac_OS%29).
If using the Java Keystore, you will need a password to protect the keystore containing the refresh token. You may want to prompt the user for this password (in a JavaFX password field) on keystore creation and use so that you are not storing it on the client.
You'll likely need to sign your application to allow it to make use of the facilities required.