Shout-Out/Fan Works

Many Fan Fics use Shout Outs - to things within fandom, and to other works, because it's all Just for Fun after all.

Harry Potter

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.
A.L. de Sauveterre's Harry Potter and the Society of Orpheus and Bacchus pushes over into Reference Overdosed, which works with the fairly tongue-in-cheek tone of the story. A short sample:
- 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.
- Draco Malfoy is encouraged to read Ernest Hemingway's Death In The Afternoon.
- The Three Musketeers (all four of them) show up in paintings to give Ron love advice, and continue to pursue the now-vampiric Milady.
In The Ollivander Children, by vifetoile, a certain theory of wandless magic is called Weatherwax magic (a shout-out to Discworld) and the Muggle character, Mark, makes frequent references to The Princess Bride and The Lord of the Rings.
In Oh God Not Again, there are several shout outs, including ones to Star Wars, The Princess Bride, and The Picture of Dorian Gray. What's most notable, though, is that at one point, this trope is lampshaded (along with everything else).

Snape: POTTER! Enough about your mythological creatures and your obscure Muggle literature!

Other

In Ringshadow's Slice of Life Star Fox fanfic Butterfly Photographs, Slippy programmed an AI into his pickup truck which has the ability to drive it. Its avatar is a face on a video screen, and its name is Max. At one point a character asks if Max is in one of the stages of rampancy in reaction to Max's slightly odd behaviour.
Disgaea: Jewel of the gods at the very begining has already gave ones to One Piece, Bleach, Dragon Ball, Soul Eater, Tengen Toppa Gurren Lagann, Chrono Trigger, Beyblade, and Metal Gear.
The His Dark Materials fanfiction Like gold to ayery thinnesse beate has Will doubling over in laughter when Lyra tells him she put a wardrobe over an opening to another world.
In The Butterfly Effect prequel fanfic The Butterfly Effect 0, the head of the Sunnyvale Institution is Dr. Emmett Von Braun.
In the JAG fanfic Abyss of the Soul, Marine Staff Sergeant Jonathan Scott Beckett had faked his death and was living under the alias "Sam Archer" when he was arrested.
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.
With Strings Attached has a number of shout-outs, including:
- Plenty of subtle Beatles references, of course.
- A line lifted from Sweeney Todd.
- A reference from a Sheri S. Tepper book.
- Several references to lines or incidents from the Flashman series.
The Fullmetal Alchemist series The Elemental Chess Trilogy has a few, both in-universe and otherwise.
- 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^[1]. And there's this quote from her "bro" Jeff:

"I'm a mog. Half man, half dog. I'm my own best friend!"

- From the same author, we have Fullmetal Eds, in which Ed exclaims "Holy *** on a ** sandwich!"
Fanfiction.net has a humorous CSI fanfic in which Ray takes 'Morpheus' as an online username, a shout out to his The Matrix role.
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.
There are tons in a A Cure for Love: Matt hums the Star Wars "Imperial March" when Kira enters the meeting room. Also when Light gets a scar on one of their misadventures of getting shot at he grumbles in his Internal Monologue that it makes him look like Harry Potter. Also in the deleted scenes Mello compares Light to the Byronic Hero Heathcliff of Wuthering Heights and his Freudian Excuse is similar in this ficverse. There's a stealth one with the Original Character V who has a vendetta. Also "Matt had just been spectacularly killed by a zombie riding a unicycle" and Near points out that "One does not simply walk into Mordor." Also when Light confides in L about his little problem and why he can't just quit: "Think of Faust, L. It's Faust on a shorter time scale."
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.

↑ Maysalee is the name of Madge's aunt, for those who don't know

[1] Maysalee is the name of Madge's aunt, for those who don't know

[1]