They seem to me to be Psychically powerful Xenos who were probably native to the Dark Angel's lost homeworld, since it's been said that they were part of Caliban's history for as long as anyone can remember. I highly doubt that they have anything to do with The Emperor, aside from their obvious subservience to an Astartes Chapter. Although, it is worth noting that they oppose Chaos. Anyway, they're quite a mystery.
Nice topic Ive always been curious about this too. As Fool of Blades said they seem to be native to Caliban, are psyhicly powerful, and seem to oppose Chaos. 40k Wiki: During the Great Crusade era, a Knight of The Order by the name of Zahariel (who would later go on to become a Librarian of the Dark Angels Legion) first encountered these mysterious creatures while undertaking a Beast Quest. He recognised these entities as the Watchers in the Dark, creatures who had existed in the ancient legends of Caliban for as long as anyone could remember, living in the darkest regions of the wild hinterlands of Caliban's forests. These humanoid entities warned the young knight to cease in the pursuit of his goals. Undeterred, Zahariel continued to undertake his quest. The Watchers in the Dark appeared to oppose Chaos and seemed, on some level, to be attempting to limit the power of Caliban's Great Beasts. Options: Xeno race with strong psyhic abilites. Former humans that (de)evolved during the Age of Strife. Warp enities and/or the collective manifestation of the Unforgiven's guilt reflecting on the Warp (which would also mean across time) Warp enities is the one that most intrigues me. The warp is not inheritantly evil, and there are Other beings that inhabit that plane. They are noted to have been around at least since the Age of Strife on Caliban though no record of them exsits of them being anywhere else (helps to rule out Xeno). Also this would help to explain the scale of their power, because we need to keep in mind that: "Jonson, who had been briefly spirited away into the Warp during the destruction of Caliban, eventually emerged and was taken into a hidden and unreachable chamber deep within the heart of The Rock by the Watchers in the Dark and placed into stasis to keep him alive." Which means that they A) had to power to take El'Johnson from Chaos Undivided and/or B) have sucessfully hidden and protected the Lion since he returned to Realspace. That would take a lot of mojo, as its pretty damm safe to assume that Chaos would love to get their hands on another Primarch. Also of interest to note, The Emperor himself came to Caliban when his Scouts found El'Johnson. Which leads me to think that either they were not on the planet, he could not sense them, or he knew that they were there but choose not to say anything. Last thing: "Jonson publicly re-named the First Legion the Dark Angels after an old Calibanite myth." Are the Watchers in the Dark the orgional Dark Angles? Who created the Myth and what exactly is it??