- Beam Me Up, Scotty!: Inverted; this manga features a version of Haruhi's famous Establishing Character Moment, but like most people quoting it forgets to include mention of sliders.
- Evolving Credits: The end credit animation changes three times throughout the run of the anime. First, on the Episode 10, the beginning of the Disappearance arc, to symbolize Yuki's identity amnesia by changing everyone into different colored silhouettes, and again on the Episode 13, where it's mostly back the way it used to be with a few changes.
- Role Reprisal: Everyone (yes, including union-only voice actors Crispin Freeman and Kari Wahlgren) from the original Bang! Zoom! Entertainment Haruhi English dub manages to reprise their roles for Funimation's broadcast dub.
- Running the Asylum: The story reads almost exactly like your typical Alternate Universe Kyon/Yuki fanfic.
- Technology Marches On: In the manga, Yuki is shown playing a PSP in her free time (or during nighttime when she supposed to be sleeping). She plays with a PSVita instead in anime.
Trivia / The Disappearance of Nagato Yuki-chan