The Transylvanian storyline having Dracula as a vampire hunter at first seems to be a Take That against Bram Stoker, but remember that Vlad Tepes III's nickname is The Impaler having him as a Vampire hunter instead of the Father of all Vampires makes sense after all why would a Vampire use impalement as a method of execution. It may also count when you consider Vlad's local reputation in Romania where he's a national hero.
The Solomon Island storyline. The reason taking Excalibur caused the Filth to invade? The light of it was keeping it at bay. Without anything to restrain it it grew to the point where it overwhelmed the other wards.
The reason why the manager of The Dream Palace in Kaidan wears a sexy sailor outfit? Her employers are the Phoenicians and the Dream Palace is their base of operations in Tokyo.
Issue #9 is dotted with references to Alice In Wonderland, with Daimon being highlighted as a stand-in for the Cheshire Cat by the Bees, and the Rabbit Killer being an obvious reference to the White Rabbit - Yuichi actually referring to her by this very name. However, though many other characters have no official tie-in with Wonderland, there are a few clear possibilities: for example, Yuichi and Harumi spend most of their days in a timeless state of objectiveless fun and paranoia, with Harumi being noted for her excitable behaviour and Yuichi easily recognized by his bizarre "space hat"; as such, they're a pretty classic stand-in for the Mad Hatter and the March Hare. For extra fun, take a good look at mercury poisoning (believed to be the origins of the term "Mad as a Hatter") and note that the symptoms include "excessive shyness, confidence loss, and nervousness" - all suffered by Yuichi!
Other stand-ins found in Tokyo may include the following: Gozen for the Duchess - both being aggressive matriarchal figures with a tendency to ramble on about morals and morality, both employing an equally aggressive cook (Akashi) and a set of underlings with a distinct lack of attention to detail (the Duchess's footman paying little attention to visitors, the Jingu Clan failing to notice the fact that they were borrowing vehicles from a death cult). Sarah is a stand-in for Alice - though admittedly, Sarah's a bit more ragged than the original Alice, having been subjected to a maddening Mind Rape while trapped at the bottom of Tokyo's subway system (for all intents and purposes, the Rabbit-Hole of Tokyo) . Finally, what with the repeated motif of flipping Tarot cards utilized by the lore entry on the Orochi Group, the Queen of Hearts can only be Lilith, with Samael/Samuel Chandra naturally representing the King of Hearts. From here, it's also possible John is the Knave of Hearts, especially given that he's deathly afraid of being caught and punished by Lilith.
During the "Headhunter" sidequest in Egypt, only one of the Marya recruits is still alive when you find him. And while you're doing "The Traitor" quest, if you pay attention, the house the traitor was based in is the same one the only surviving recruit lived in, and that same recruit shows up at the end of the mission as the Aten informant. Which explains why all the other recruits are dead or Filth-infected.
When reading the Buzzing and the Black Signal lore from Issue #9 you will notice that the Buzzing often ending their message in sudden mess of unintelligible characters while the Black Signal's lore opens with the hiss of radio static. It makes sense when you realize John is literally hijacking the Buzzing's frequency.
The final mission of issue 10 shows how John was chosen to be carrier of the Filth bomb and what happened after. The fridge horror comes in you realize that John was not the first choice and that it could have been Yuichi that it all happened to.
In one lore entry, the bees say that the Third Age ended "under tentacular skies," so when Lilith says the Third Age ended when a barely woken Dreamer "strangled the world," it might not entirely be a metaphor. The end of the Third Age must've been far more horrific than a 'normal' cataclysm.
The Dragon Lore tells of some of the things they were doing over the years, one account is of how they were injecting rats with the black plague during the dark ages. Now this is eerie enough but goes with the notion of seemingly chaotic acts all fitting into social engineering, gee a secret society is willing to kill masses, shocker... But then in The Ankh, Dr. Klein makes reference to his experiments being "The most important Filth event since the Black Plague."... Which means... The Dragon were ACTUALLY SPREADING SOUL DEVOURING, REALITY CONSUMING, BODY POSSESSING, LITERAL NIGHTMARE FUEL! Whether they knew what it was at the time, to say nothing of how trust worthy Klein is may offer them some level pardon but god damn!