Both Sues trade notes on pets, and Squee! when they see Empire Kirk in his sleeveless glory. Empire Kirk's response? "Damnit, Spock! If you don't get rid of at least ONE of them, it's the ice planet again!" Closing his eyes in defeat, Empire Spock goes, "Alright, we'll take ours back."
Spock failing to murder Ensign Sue with his phaser (set for Pocket Deathstar).
Uhura's expression when she fails a Uriah Gambit involving Ensign Sue and Klingons.
Ensign Two has already racked up a few of these given the circumstances of The Doctor having an extremely awkward team-up with Spock and Kirk, which is humorous in itself. Not many chapters in, one of the Sues (who is Part Time Lord) snatches the TARDIS while the three were shopping for Pokéballs in the Pokémon Universe, but Kirk's line in response to being stranded just seals it:
Even better, during Spock's team's capturing montage, all of the Pokéballs used are variations that make sense for that particular universe, such as a Dusk Ball for Buffy the Vampire Slayer, a Timer Ball for The Da Vinci Code, and a Master Ball to capture a Sue-transformer.
Shortly after the above happens, Kirk (Who is still in the middle of his HeroicBSOD in his cell) meets a strangely-familiar face in a Starfleet uniform who appears in his cell. Turns out its not exactly who he thinks it is.
Kirk: Your face... That uniform... My god, areyou...?