Hi James,
Not sure if you had a chance to read up on the SSO support within Thingworx, but it is an extension that exposes hooks to a user so they can build an SSO Extension for their particular need.
Also if you haven't seen it yet, the new 6.0 comes with a full Java Doc: http://support.ptc.com/cs/help/thingworx_hc/thingworx_6.0_hc/