A probably intentional one late in Pantheocide: the engineer in charge of blowing up Heaven's Gates is Lieutenant Chard. (Lt. Chard was one of the heroes of Rorke's Drift.) No, it's not the original Chard, he's a modern (first-life) Officer of Engineers, but the coincidence is striking.
Orphaned Series: While the first two books are finished, it looks like the third will never get released. The first two books were pirated as a deliberate (and successful) attempt to destroy any chance of them being published by a regular publishing company (one such had agreed to publish them but pulled out after the piracy). Since the author has a large number of personal and business commitments, this means that his attention has to be centered on work that has a chance of generating a financial return (his TBOverse series sells very well). The third book may be written in time, especially if the pirated torrents vanish but they will be posted on HPCA rather than SDN since the thread there that the series was posted in has been locked (for people discussing the torrentage/future of the series too much...) and a new one isn't allowed to be created.
On a few occasions, characters will note that they have no idea what the scientific principles behind seemingly supernatural events are so they're just accepting for now that they exist while working on the problem in hope of getting an answer. This normally indicates a point where the demands of mythology and science are contradictory to the point where the author himself is having trouble coming up with a plausible scientific explanation. Word of God says that, as far as possible, everything in the story has a rational scientific explanation but limited exemptions are made in order to give the mythological creatures at least some hope of survival.
In the story, it's mentioned that Elhmas possessed three individuals in an attempt to influence humanity. The first two are specifically stated to have been Jesus and Mohammed, but the third is never mentioned. The author notes that he didn't have anybody specific in mind when he wrote it, but that it could pretty much be anybody.
What Could Have Been...: Ironically, the author revealed that Armageddon??? had been rigged to give the demons the best plausible position — had human air support not been available, humanity's response would have been nuclear-tipped surface-to-air missiles:
Without aircraft around, such weapons would have been free right from the start and nuclear initiations would have been commonplace. That means they'd have been used on the ground forces as well. Dis and every other major population centers would have been nuked as a matter of course. The story would simply be one of a nuclear onslaught and then humans mopping up the pieces.
Word of God: Both "The Message" and the nature of some of the author's discussion of elements of the novel cannot be completely explained/shown (or at all, as far as "The Message" is concerned) since Stuart knows he could simply never do it convincingly.