You know, I was rather curious how the AI Jor-El in the Fortress could know what was said between Clark and the spirit of the dead Jor-El when he had the "near death experience." But I was talking with a friend of mine a few hours ago, and he had an interesting observation based on a single question.
Where did Zod get the blue-K dagger?
And the obvious answer would be at the Fortress. So if it was part of the Fortress, it stands to reason that the AI Jor-El was linked to it. Which is why he was able to maintain that state Clark was in, and contact, for as long as the dagger remained in his gut. Hence why it all snapped back the moment Lois pulled it out.
Now, when AI Jor-El lost contact with out-of-body Clark and the skies there changed? Quite possible that it was Jonathan, one disembodied father fighting the other for the sake of their son. So yes, I still think it is possible we may see him resurrected for episode 200. The odds are stacked against it, I can see. But who knows? It is still within the realm of possibility. And provides a good symmetry since he died in episode 100. It would really shake up a few things if he did. And he did say he would do anything to get a second chance this episode, didn't he? And hey, I am not afraid to be wrong. But who is it that would or could do this? Someone/thing that obviously acts with a balance, since it was what sent Lex's soul back too (which the kid likely got. Notice the knight in the fire? The kid is really evil too). So maybe whatever it is likes symmetry too.
But as to the coming darkness and Clark being a force for evil? With the appearance of Darkseid I am reminded of something that has happened in the comics and the animated series. Darkseid turned Superman and made him into his champion and sent him out to conquer in his name. In both stories he is able to eventually overcome the control and become himself again. Perhaps a similar fate is in store for Smallville's Clark? And Jor-El doubts his ability to overcome the domination? It seems to fit. We'll see though.