Daysleeper, I was making the assumption that it was the pilot that had lost access to the information. Obviously if the controller has doubts about the accuracy of the mode C data there are well established procedures to follow. But if the pilot has conflicting info and there's nothing to suggest that the mode C is inaccurate then a cross is the best way to pin down which altimeters can be relied upon. And even in the simplest aircraft fit the encoding sensor is separate from the altimeter display in front of the pilot.
BOAC's point about RADALT is good. When I offered my first thoughts I had in mind a less sophisticated avionics fit but in such a situation every bit of help is useful.
I avoided woocash's question about declaring an emergency originally because I didn't have a lot of time but I while it's clearly up to the pilot to establish the severity and seriousness of the problem I'm not sure that it will always count as an emergency. In good wx without additional problems navigating I would class it as an unusual event requiring special handling (I'm speaking as a controller). In solid Cat III conditions at all practical landing sites it's a very different situation. Certainly the pilot should tell the controller - good Team Resource stuff to call on anyone who can help - and then I would expect a solution suitable to the conditions to be worked out.