the new GS will be out in 2011. The rumour (from their R&D in Munich - my sisters boyfriend is working there in the lifing department) is that indeed we have seen the last iteration of the boxer engine. They need more clean power out of it and are not able to achieve it either by increasing capacity or increasing the engines efficiency in thermodynamic terms (making the engine produce more work and less heat out of its fuel). That means they need to look at other configurations.
I haven't heard of any KTM engine rumours, though its well known they have poached many people from BMWs R&D over the years (ktm now has over 200 r&d staff up from 25 in 2001). That has no link to any BMW usage of KTM parts whatsoever, and why would they do it since they have the funds and the know how to design themselves.
The only story that i have actually been told by him (and is a non kept secret) is that a larger version of the 800 parallel twin is already on test benches and is watercooled, quiet, vibration free and will be the cleanest motorbike engine ever made. What they are going to do with it and if its due to fit a new RT, ST and or GS is to be seen.... I would guestimate a yes, even if bro in law to be won't say an inch more..