Arabella and Zsenya's epic fanfiction After the End contains a significant Shout Out to an in-fandom joke: in the Shipping wars, the Good Ship Harry/Hermione had the iconic symbol of pumpkin pie. In After the End, (a fic that is very Ron/Hermione, based on a website that is strongly geared towards the same) Ron angrily tells his mother that he hates pumpkin pie.
The prologue refers to a tapestry with the cast of The Lion, the Witch, and the Wardrobe on it (with the implication that Harry may be descended from the Pevensies).
Colin Creevey dressing up for Halloween as famed (Muggle) photographer Annie Liebovitz.
Decks Fall Everyone Dies. Examples: "Reverse card open" is a shout-out to the MAD videos that feature Kaiba repeating that line. Yami's line calling dice "rolling bones" (astragali) is a shout-out to the manga.
In the first story, the three main characters sneak into beseiged Central City using a hot air balloon, which is a call back of sorts to the 2003 anime adaptation.
Edward Elric's son is named Lucas, after Luke Triton from the Professor Layton games.
The Brotherhood anime showed a photograph of Roy Mustang after the end of the series in which he has a mustache, for reasons unexplained. Many members of the fandom prefer to believe that, as the picture in question belonged to Ed, he had drawn the mustache onto it; this epileptic tree is firmly planted in the fanfic.
In Mary Mary? Quite Contrary!, there are many shout outs made in the "Sparkly Shiny Alchemist" story. For one thing, the protagonist's full name is Christiana Sophia Maysalee Thomas*
Maysalee is the name of Madge's aunt, for those who don't know
W.I.T.C.H. Fanfic Kieva Lynn's Season Three features C'thulu in one episode. The episode title "The Telemarketing Call of C'thulu" is a play on the title of Real Ghostbusters episode "The Collect Call of C'thulu." They even beat him in much the same way.
In Clash of the Elements there is one to Super Mario Bros. Z in Chapter 45 of Part 1 More specifically, the act of having the Star Spirits appear and using their energy to power-up Mario and the other heroes, a concept which, while it didn't get to appear in the actual series, at least got shown in the intro. Thankfully, the author gives Alvin-Earthworm full credit for the idea instead of claiming it as his own.
