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The blood on the wall re-appears in chapter 81 after showing up in the Silent Hill arc.
Early on, The Stinger at the end of each chapter was, "Review, Haruhi-worshippers! Your yellow ribbon-wearing goddess demands it!" One reviewer pointed out that this was incorrect, and that Haruhi wore a headband with yellow ribbons on it, so about 50 or so chapters after this was pointed out, the writer corrected it to what you see at the top of this page.
As of Chapter 85 it's now, "Review, Haruhi-worshippers! Your goddess with the yellow headband and ribbons demands it!"
Comically Missing the Point: Phoenix asking Ryoko if the blueberry muffins were any good after she mentioned Kino "stealing" a knife she was looking at and taking a different kind of muffin (which happened to be her favorite) for free after a purchase. The author lampshades the fact that it was simply a minor detail in an already idiotic revenge story.
Did You Just Punch Out Cthulhu?: Chapter 81. A giant cheesecake starts destroying the school, and the cast tries to destroy it with no such luck. A fat AU Haruhi comes from another fic of the author's, and manages to devour the cake in two minutes.
Disproportionate Retribution: From the Court Case arc. Long story short, Ultros is accidentally sneezed on by Haruhi and doesn't receive an "excuse me", so he sues her for plagiarism and hopes to receive money from her while Haruhi is imprisoned where her pancreas is eaten by a Skarmory daily.
Also from that arc, there's Haruhi demanding that Imouto dies for insulting her honor and in the daydream when an original character crushes a guy's windpipe for chewing too loud.
The Ditz: Naru can be this at times, as can Kyouko.
Doorstopper: At over 300,000 words, it is longer than the longest Harry Potter book and still incomplete. Even more amazing, most of that length is from the two most recent Story Arcs.
Fan Nickname: Invoked. After their first appearances in the fic, the author started referring to the Computer Club President and the Student Council President as TCCP and TSCP, respectively, on the grounds of being easier to type. Also, the bespectacled boy whom Kyon saves in the seventh novel is called Four-Eyes here, because he is an exceedingly-minor character who doesn't get referred to by a name or nickname of any kind. Superstarultra and his friends wanted to be able to refer to the character in fan fiction, but did not want to come up with a name for him in case it got Jossed.
Flat "What.": Happens every now and then. Haruhi being crushed by a blimp, for example!
Yuki's response to Ultros' reason for suing Haruhi. It's INCREDIBLY stupid.
Follow the Leader: This fic has inspired some other crackfics, and was itself inspired by a Code Geass fanfic titled You Got LuluRolled.
Forgot Flanders Could Do That: Chapter 84 begins with Fujiwara and Kyouko actually trying to get Kyon to join them and transfer Haruhi's powers to Sasaki. After so many chapters of Fujiwara completely neglecting his mission and Kyouko being a lovestruck idiot it can be kind of shocking to see them like this. However, bits of their Flanderized characterization still appear, such as Kyouko invoking Sasaki's name as if she were a deity when she's caught by surprise.
Freudian Slip: Hermes' "Come on me" line from the court case arc (instead of "come with me"). Justified if you know the series.
Noodle Implements: The fetish chapter, where Haruhi has a half-finished fanfic with all the things she wants to do to Imouto involving: whipped cream, a feather-duster, chocolate sauce, scented candles, strawberries, a watermelon, a chinchilla, a golf club, and half a quart of orange sherbet. The first half of that list seems fairly normal, but somewhere around the watermelon it starts to meander into this trope.
OC Stand In: Four-Eyes, in the court case arc, is actually a minor character from the novels who was not even given a name. It's a Downplayed Trope though, in that he is no more important here than he is in canon.
Off the Rails: Chapter 81, written one year after the fic started, is quite possibly crazier than any chapter before or since. It's even the chapter title.
Haruhi: "Don't feel sorry for me, Mikuru. Feel sorry for Konata! She's forgotten the pirate ways of old! Has a big, fancy, mechanical ship and everything... What kind of self-respecting pirate uses torpedoes?"
The Silent Bob: Averted with Yuki, but until recently, this (sort of) described Kuyou, who rarely spoke, and when she did, it was in underscored text. Word of God says that she'll talk normally more often since the novel 10 preview came out.
Snap Back: Occasionally. For example, at the end of the AVTT arc, Tsuruya is pissed at Mikuru and Yuki. Next chapter, everything's fine and dandy. Subverted when some incidents like this are brought up again.
Unsuspectingly Soused: During Chapter 68, Emiri decides to liven up a sour Ryoko at a party by lacing her drink with a special type of data-program. Moments later, she is babbling about her misfortunes and even proceeds to make out with an equally-hammered Kyon.
Weaksauce Weakness: Towards the end of Chapter 81, the author is causing absolute chaos, having all the characters on the ropes. He is finally defeated by a hentai doujin, which squicks him out so much that he leaves of his own accord.