Tobi
This destroys the theory that Mandus killed his sons in the Temple, as a sacrifice.
Anyway, so far we have few theories, most of them rely/using Mandus insistence as a basic ground:
A ghost - Mandus was a ghost (second part of the personality?) all along and his dead body is in the iron lung sarcophagus. Makes little sense since we can interact with the world and Pigs can hurt us.
Hallucination/mental play - my favorite. Mandus builds a Machine on the bones of his children, he himself becomes part of the Machine, a machine itself, lying in the sarcophagus. His personality splits on two - The Machine and Mandus. Since he is the heart of damned device, each time when these personalities clash they cause havok to actual machine: Mandus wins at some point, "sabotaging' device and shutting it down. The Machine manages to shoo him, but in order to restore device it needs Mandus. So it "wakes" him up, and with trickery get his help in restoring "power" again (I assume the consciousness of his body in the lung can somehow operate machine). Second personality, ie Mandus. realizes it and he fights Machine again. Remember how he talks about making himself "whole again"? In the end I think Mandus wins, he accepts the truth, what he did, he accepts his damnation and thus completely takes over the machine (1st personality), becomes whole again and shuts down The Doom's Device since nothing can prevent him to do so anymore.
Now, what is about what we see in-game, all the locations and actions we do? This is the brain's interpretation of the clash of the personalities that happens in his mind. The notes we find is the memories his 2nd personality uncovers, it is all in his head. Pigs are obstacles, but that does not mean they don't exist in outer world, they do.
A cadaver
Somehow Mandus either managed to split himself on two (???) or may be he made a Pigmen out of himself, with second personality. That explain many things well, but what about that damn hand that hold the lamp? It is not a pig hand. Although, even there could be some explanation, even if far-stretched:
1. Instead of making a Pigmen he used professor's body to put part of his personality into. That does not make much sense, but it would if there was an orb actually involved into story. But it is not, we don't see it at all, seems like it was cut just like 2 other endings.
2. Remember the note about mirrors? Perhaps Pigmen can recognize themselves as manpigs only in their reflections, but when they look upon others or themselves their mind plays trick and they see humans. Too thin, too weak theory, though.
Either way, even though Orb's existence is mentioned, it is not in the game. We can't see it anywhere or read about it directly (except one vague note), but its presence would explain a lot. As I mentioned here:
http://www.frictionalgames.com/forum/thr...#pid259111
seems like the machine was supposed to be powered by Orb originally.
Did I miss any other theories?