The prequel also has Haley's ID number on her mugshot as 24601.
Book D: Snips, Snails and Dragon Tales
In the strip from the final issue of Dragon, the Order go through a door labeled "Do not open except in case of parody or other fair use". Behind it are stick-figure versions of characters from various cancelled Dragon comic strips: Finieous Fingers; Wormy; Snarf and Telerie (SnarfQuest); Phil and Dixie; Yamara; and the Knights of the Dinner Table.
Larry Gardener (see below) puts in another appearance, this time with friends.
In a sequence in which the Order and their Fourth Edition counterparts take on other pastimes, the Vaarsuvii blast Superman with magic, the Durkons handle a certain sparkly vampire, the Haleys plot an attack on Mario and Roy attacks a cloaked wizard, scattering Magic: The Gathering cards everywhere.
Eugene: Ooooo, yes! And while your friends collect the seven magic spheres to wish you back to life, you can train with the secret martial arts master who lives here in the afterlife! Roy: ... Really? Eugene: No, not really, you moron! Does this look like Dragon Ball Z to you?!? Roy:Could have fooled me, that last battle took long enough...
If a shout-out to Egyptian mythology counts...
Roy: ...I don't suppose we could just weigh my heart against a feather instead? Bureaucratic Deva: Oh no, we haven't done that for years. The scales are a bitch to calibrate.
Therkla leads Elan's party into a Captain Ersatz of a Dharma Initiative station from LOST, complete with the iconic Dharma Initiative logo (with a smiley face in the middle) and a sign on the wall that says "Welcome to the Greg Initiative, Station 32: The Smiley Face." When they leave the station in the next strip, there's a bonus Take That:
In the same strip, the punchline has Cyclops of X-Men taking the place of the cyclops from The Odyssey as a Visual Pun. The title "Meanwhile His Teammate Was in Rhodes" refers to fellow X-Man Colossus.
In Comic #906, Nale utters the phrase "Not a cloud in the sky" as a signal to Zz'dtri to turn on Malack. Just for reference: "Above all Spain the cloudless sky" was the phrase broadcast to signal the start of Francisco Franco's mutiny in 1936.
In Comic #919, Vaarsuvius comes back from Hell and one of the first spells the wizard casts is a Wall of Fire encircling V's friends. The title of the strip is "I Went Down, Down, Down", a lyric from the Johnny Cash song "Ring of Fire".