The title of Chapter 11 (Herioc Antics Begin arc 4) is Yeah, It Went There
After Ryouko gets chibified, Yuki needs to prepare something to contain her so Kyon could be calm enough to sleep. The container is a specially prepared cardboard shoe box, thus making it a literal Cardboard Prison.
In combination with Expospeak Gag, a bit of narration from Yuki's perspective notes that "In addition to the cover being the least adequate part of the book to judge the contents by, according to contemporary human adages, she knew that thematically, elements were redone specifically to catch the eye or try and sell the contents as a product to an unwary consumer." In other words, Covers Always Lie.
Kanae's, and now the SOS Brigade's, world have been invaded by the Combine.
The title of Chapters 47, 48, and 49 are "Resonance Cascade", parts 1, 2, and 3, respectively, and Wataru mentions the Seven Hour War.
Yuki's response to Haruhi wishing for Kanae to be able to control her slider powers better and find her way home again is to warn of "unforeseen consequences."
Yuki: "I cannot determine parameters of dimensional sliding. Because of this, it is not possible to determine the effects of attempting to initiate a change in Michikyuu Kanae's abilities; attempting to alter or tamper with them may cause unforeseen consequences."
Takahashi: I don't think about that, and neither should you. note The (in-)famous answer given to the question whether Ranma can get pregnant
The brigade talk about black holes and Yuki comments humanoid interfaces can't preserve themselves unassisted there. Haruhi asks Yuki if they are her kryptonite.
From Chapter 2:
Kyon: "It's not like I've asked Asahina-san to let me go back and give myself notes on tests I did poorly on. Or I've come back from the future to warn myself about upcoming pop quizzes. Really, while it's useful to have access to that kind of power, well.... With great power comes--" Haruhi: "Don't even try and quote that movie at me," she warned him.
"...but I digress. When you get that feeling, you know the one, in the back of your head? The one that makes you think something is off about the situation? It may be right. Granted, you may also be tumbling headlong into a fit of paranoia that will end terribly for you and everyone you love. ..."
In an early story, one of Sasha's closest friends comes under the auspices of an unkind guardian. Sasha and her remaining friends must prove the mistreatment of her friend. When this proves to be difficult, Sasha's love interest - Ichigo - devises a plot to make the guardian ill enough to be sent to a hospital, thus freeing their friend.
Probably Minagoroshi-hen rather than Tatarigoroshi-hen. In Chapter 50, Kyon's father references the events of Minagoroshi, specifically Keiichi's attempts at saving Satoko.
From Chapter 47, after Kyon is called out by Wataru:
Taniguchi: And he just ran out of class? Amazing! That guy's hot-blooded for sure! He is one bad mother— Yanagimoto: Shut your mouth! Taniguchi: Aw, I was just talking 'bout Kyon!
In Chapter 40 Tsuruya made Haruhi outline the plot of 5 Centimeters per Second in front of Kyon so she would realize how much of a bad idea was to leave certain things unsaid. That's right, a character used shout-out as a plot point to encourage another character to pursue plot (and romantic) development. It's that kind of cast.
Also from Chapter 62, Taniguchi wonders aloud if the New Transfer Student in their class is Kyon's "new fiancιe". She's not, but he gets points for getting close to the truth. The second transferee fits the profile.