All Your Powers Combined: Eventually there is a character who is descended from every member of the original SOS Brigade, and thus has all of their powers.
Ascended Extra: Kunikida turns out to be part Humanoid Interface, part Time Lord, part Saiyan, and part Vulcan, and plays a major role in the later arcs.
Beige Prose: One of the author's main problems with the story.
Berserk Button: Nobody in the Asahina-Nagato family takes kindly to anybody else in the family being threatened. Also, Yuki in particular happens to share our hatred for Endless Eight.
First Kiss: Happens at the start of Yuki's and Mikuru's first date.
Foreshadowing: By the end of the first arc, Original!Kyon is acting strangely smug. In the second arc it's revealed this has led him to become Fujiwara.
Jossed: Let's just say that the events of The Surprise of Suzumiya Haruhi reveal that there is no way that Original!Kyon could possibly have become Fujiwara.
Laser Blade: Mikuru and Kyouko fight each other with these, because SiFi gave the story's one hundredth reviewer the right to include a plot element as a prize, and that is what said one hundredth reviewer chose.
Mr. Exposition: Original!Kyon. Whenever someone takes a chapter to explain something, it's titled "Kyon Explains Everything, part X", regardless of who's explaining.
Mythology Gag: Several references to the original draft, particularly its inclusion of Dracula. He finally makes an appearance in the third arc.
Name's the Same: Kyon and his sister are actually descendants of the original Kyon and Haruhi.
Small Name, Big Ego: The writer himself. He has no problem with (and is actually quite fond of) taking potshots at much better writers, and this page was basically a love letter to his ego before it was cleaned up.
Though the writer has since disowned the fic, and is thankful for the cleanup despite still considering some of the edits to be kind of harsh.