A rather unusual example. Uhura in the 2009 film is played by Zoe Saldana, but in comic 7, she's seen reading an Ebony magazine with the original actor Nichelle Nichols on the cover.
The same kind of example in Sulu's case. After George Takei came out of the closet, some fans assumed his character was also gay. Word of God has denied this claim, but that hasn't made certain artists rule out the possibility entirely...
Ensign Two features an appearance by Sherlock Holmes—specifically, the 21st century version of the character from Sherlock, played by Benedict Cumberbatch. He helps them figure out how to stop the Sues and leaves, but not before sinisterly predicting that he and Kirk will meet again. This alludes to Cumberbatch playing John Harrison/Khan in Star Trek: Into Darkness.
Art Shift: During the fourth comic, when Sue narrates.
Mostly averted in the world-hopping in Ensign 2.
Author On Board: Played with. Although Ensign Sue has all the usual qualities of a Mary Sue, she has somehow popped up in a universe where all the other characters don't follow the usual rules of a Mary Sue fic. Except for God. And it's implied that their minds will be warped if they spend enough time around her. In the Harry Potter universe, the other characters are indeed acting like the typical cast of a Mary Sue story.
Back from the Dead: Ensign Sue, who was killed off in the end of the first chapter. God-Mode Sue didn't just conjure alternate versions of her throughout the multiverse. The original Ensign Sue still exists as the Sue of the Harry Potter universe and reveals her old medical uniform after reuniting with Captain Kirk.invoked
Also counts as a Hidden Villain since (of the protagonists) only the Original Sue knows about her.
Big "NO!": Kirk's reaction to Brainwashed and Crazy Spock's claim that Kirk is himself a Sue. Bonus points for the scene being a Star Wars reference. He gets a second in the opening of Chapter 3 when he gets razzed by Empress Sue as he's doing his Captain's Log for getting in touch with his inner Sue..
Black Hole Sue: All Sues are theoretically capable of being this.invoked
Brainy Baby: Apparently, even as a newborn infant, Ensign Sue was able to escape the destruction of the Kelvin.
The universe where Ensign Sue is found in the sequel is the same one we saw her end up in the original: Harry Potter.
In the original, Ensign Sue states that she was raised by worms (inside a wormhole!), and that they died as a part of her tragic backstory. In The Wrath of Sue, The captain is enraged by her calling him James instead of by his title, especially because of the crisis she brought upon them, and orders her locked in the brig. Her response is "This is worse than when the worms died!"
Canon Sue: Some of the Sues are canonical characters, including:invoked
Played with in Equestria. We see Twilight Sparkle included with a bunch of bad original characters, but we never see if she gets captured or not (though it is heavily implied).
Cat Girl: Anna Mae Sue seems to have this trait. Doesn't hurt she speaks in part-Japanese as well.
Cerebus Syndrome: A minor case. The webcomic is still quite silly, but while the first story was just about Mary Sue being put in a world that knows how ridiculous she is, the second story has her going through a Heel Realization and includes moments such as Wolverine stabbing The Doctor in the back, on panel.
Cliffhanger: The end of Chapter 1, where we see that Mary Sue has died, but she meets God Mode Sue, who sends her to the Harry Potter Universe. Then Chapter 2. Empress Sue has the Infinity Gauntlet, Wolverine Sue stabbed the Doctor (who then regenerated into Eleven), Ambassador Spock is frozen in carbonite, Spock has been brainwashed, Kirk is in a Heroic BSOD after being told that he is a Canon Sue, Ensign Sue has broken down in her cell after discovering she no longer has powers, and God Mode Sue's plan appears to have succeeded.
Chibi: The whole comic is drawn in this style. Which, of course, makes everything much funnier.
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...
As per Canon in the Continuity Reboot, Captain Kirk lost his father from the destruction of the USS Kelvin and spent his youth angry at the world. Spock mentions his tragic past as proof of Kirk's apparent Suehood.
Ensign Sue was also a victim of the Kelvin's destruction. She was then raised by worms in a wormhole! And then the worms died...
Expospeak Gag: Mary Sue reveals her dark secret to McCoy: she has pedal transient paresthesia! Her foot's asleep. Also a Continuity Nod to Star Trek IV, where McCoy uses fancy terms for cramps to get through a hospital with a crewmember feigning illness.
Kirk: We don't know if they have similar appearances, but they should all exhibit reality-warping powers... Fantastically and unbelievably capable, playing by their own rules with little to no consequence, and doing things that just shouldn't be possible.
Genre Deconstruction: If Mary Sue fics can be called a genre. It starts by showing how characters might really react to someone who acts like Mary Sue, then goes on to show what actually makes someone a Mary Sue, and what might happen if such a character suddenly lost their Sue privileges. All while maintaining a healthy amount of humor, of course.
God-Mode Sue: Naturally, Sues can do anything, even things that the Word of God for a given fictional universe says is absolutely impossible, like defying All Deaths Final. The leader of the Sues is very literally this. When the Sues take over, Spock says that there are no more rules, and the universe is free of convention.invoked
Gratuitous Japanese: Anna Mae Sue(-chan) the Sue of the Pokémon world in Ensign Two speaks almost exclusively in sentences with random and horribly broken Japanese sprinkled in.
She later contacts the bridge and her mangling of the language (including using "boku" instead of "watashi") break Sulu's brain).
Nice Job Breaking It, Hero: They kill Sue, but God turns her into a Harry Potter Sue and creates Sues in many other universes. Later, Kirk's frustrated decision to throw Ensign Sue into the brig puts a strain on the relationship between him and the only Sue who was sympathetic and helpful to him.
Not so Above It All: Sulu reacts exactly how you'd expect a real Japanese person would to Sue's more obnoxious fangirl tendencies but he himself daydreams about Kirk in a similar way to Ensign Sue's Yaoi Fangirl mode.
Not-So-Harmless Villain: When we are first introduced to Empress Sue of the Terran Empire, she is just as oblivious as any other Sue, and while a self-described evil doer, her definition of "evil" is entirely composed of style. But when she reappears in the sequel, she's entirely capable of beating people up on her own and teamed up with the murderous Wolverine Sue.
Obliviously Evil: The Sues may threaten the fabric of the universe and gradually warp the minds of everyone around them, but most of them are unaware of this and Ensign Sue acts guilty when told about it. After getting Brought Down to Normal, Ensign Sue becomes significantly less oblivious and prompts confusion from one of her sisters when she asks why their actions are making everyone else upset.
Pieces of God: Travelling into the mundane dimension is enough to make God-Mode SueBrought Down to Normal. To bypass this, she sent pieces of herself across the veil. These pieces manifested as the Sues. Most of the Sues are connected to her thoughts. The only exception is Ensign Sue, due to being the first piece made and thus a Flawed Prototype.
Plot Armor: Three guesses, and the first two don't count.
Plot Hole: Sue's power is capable of creating these in order to make her "perfection" possible. For example, Ensign Sue is the youngest Starfleet officer ever. And yet, just like Kirk, she was somehow a victim of the Kelvin's destruction, even though that should make her too old.
Psychopathic Manchild: All of the Sues have a childlike disregard for the extremely dangerous consequences that should result from their whimsical actions (which somehow usually don't happen thanks to their nature), but Anna Mae in particular takes this to sociopathic levels when she steals the TARDIS, attacks the X-men, and kidnaps Ambassador Spock, freezing him in carbonite.
Reality Warper: This is what makes Sue go beyond a mere annoyance and present a true threat. Not only does the universe gradually shift itself according to her whims to make her perfection possible, but given enough time, she will warp the minds of everyone around her.
Raised By Worms: Apparently, Ensign Sue was found and raised by worms living in a wormhole.
"And then the worms died..."
Rant Inducing Slight: Kirk finally loses it toward the end of the second episode when Ensign Sue calls him "James" one too many times. The opening to Chapter 3 has Kirk unsure where Sue's loyalty is, or if she's willing to help them in the wake of it.
Red Shirt: The only possible way to kill Ensign Sue, as the increase in mortality rate is the only concept stronger than her ability to bend reality.
Specifically defied later on during the sequel. Only named senior officers go around catching all the Sues because of the likelyhood of this happening along the way.
Relationship Sue: In-Universe, Ensign Sue clearly sees herself in this light, including asking Uhura to "step aside" form her relationship with Spock and constantly insisting that she and Kirk share a deep love.
Skyward Scream: Kirk's reaction to a brainwashed Spock's allegation KIRK is a Sue, too.
The Sociopath: Anna Mae Sue has become this, revealing that she froze Spock Prime in carbonite in the stolen TARDIS, describing it as "kawaii!" She also doesn't even try to listen to or empathize with others, something not even the original Sue was guilty of.
SpaceX: Her Spunicorn is "like a unicorn, but it's in space"!
Thinks Like A Bad Fanfic: Sue clearly sees everything as if it's being manipulated by a Sue-loving author. Thankfully it turns out she won't be made right unless people are subjected to too much Sue-presence but sadly, the Harry Potter characters were....
This Looks Like a Job for Aquaman: The actual Aquaman is delighted when asked to help out with something real. It didn't take long at all to find the superheroine Sue though.
Wham Episode: The 30th strip of "Ensign Two": Spock, the Doctor, and Wolverine board the TARDIS to confront Anna Mae Sue, only for Mirror!Sue to appears and knock Spock out with the Infinity Gauntlet and Wolverine showing his true colors by stabbing the Doctor. HOO, boy...
And when Spock gets back to the Enterprise, He's become a Sue.
What Have I Done: Ensign Sue when she realizes that she will be responsible for the Sues conquering the Enterprise.
You Are What You Hate: The Logic Bomb a brainwashed Spock drops on Kirk is this. The opening to Chapter 3 has Empress Sue razz Kirk during his Captain's Log, telling him "You're really getting in touch with your inner Sue!" and making him drop a Big "NO!" in response.