Cry for the Devil: Ensign Sue starting from Episode 2 Strip 27. Stripped of her powers and rejected by the crew of the Enterprise, she finally gets a genuinely sympathetic moment. Then Anna Mae Sue releases her from the brig as the bridge crew are paraded by them in chains, Spock with a phaser behind them being snuggled by Wolverine Sue...
One of the many Alternate Sues in the finale is a My Little Pony (from Generation 3.5). That strip was drawn exactly two weeks after a certain other show debuted, almost immediately thereafter caught the attention of the Periphery Demographic, and...guess which fandom is now completely flooded with Mary Sues? The comments section is especially hilarious.
Nightmare Fuel: Almost all of the Doctor's deaths are played for comedy, but two are very disturbing. The first, where he's stabbed in the back by Wolverine and when he dies by Khan's hand when Khan twists his head all the way around to break his neck.
The reveal of the sue-ified Spock was mildly creepy. Sue-ified Chekov, Sulu, and Uhura were scary. Sue-ified Korra and Sonic the Hedgehog? Outright terrifying!
It also slams home the idea of altering people to make them love you means that it's not really them who love you anymore, and you'll have to live with the fact that people only like you because you forced them to.
They Changed It, Now It Sucks: God Sue seems to share her opinion about Zachary Quinto being Spock as some of the fandom does, as she refers to him as "younger, less sexy Spock".
Uncanny Valley: Some of the characters seen as Sue-ified due to their changes. Korra, who's been made much skinnier, is particularly creepy looking (not to mention that her stance is eerily similar to how she looked when Tarrlok used Bloodbending on her).
Unpopular Popular Character: Ensign Sue. She's difficult to hate because she's comedic and just so... flippin'... cute! It's like trying to hate a 5-year-old playing make-believe. Her later Character Development makes it hard for even Kirk to hate her later.