Offhand I don't recall any such elements in Earth: Final Conflict.
I mean, there were those nuts who worshiped the Companions. And some of the tech (such as memory transfer) was pretty farfetched. But it was technology, ultimately.
Of course, the line between supernatural and sciencenatural is extremely blurry.
That's a good point. You can explain away a lot of supernatural elements by having them be 'part of an alien race's natural abilities'.
I'm going on the premise that even an alien species must submit to the natural laws of physics, chemistry, biology, etc... So in a way that disqualifies EFC as well (though I am quite fond of the show).