A chapter named Murder Most Fowl from the Time Paradox is also the title of a book. There's also two references to Lord of the Rings in the same book. 'all real, just like Lord of the Rings' and 'like one of Tolkien's creatures'.
Af books have several references to great criminal of older date Jim DiGriz most obvious are
book 5 - where Artemis returned from time travel several years later than he came and find his mother Angeline has twins
book 2 - When Artemis use his blood to fake shooting his father.
Foaly tells his nephew Mayne in the last book, "Listen, nephew, if you want to strap a horn to your forehead and go to conventions on the weekends, that's completely fine" and references a miniseries about unicorns that Mayne is rather obsessed with. Seems the Lower Elements have their own version of My Little Pony: Friendship Is Magic.
That, or Star Trek, since Mayne also speaks "Unicornian", an In-Universe fictional language (compare this to fans of Star Trek speaking Klingon).
In the final book, Foaly pokes fun about the fear of the number four Artemis had while suffering from his Atlantis Complex by telling him "May the fours be with you."
Two companies crossed over between the Artemis Fowl series and The Supernaturalist
Phonetix: originally mentioned in Eternity Code as the main competitor to Jon Spiro's Fission Chips
Krom Automobiles: originally mentioned in The Supernaturalist makes an appearance in Last Guardian as a fairy company that bought the former Koboi Labs building.