Here's a list of some of the known fan comics, written runs, screenshot runs, and misc runs inspired by Nuzlocke Comics.
NOTE: Please refrain from using this list for shameless self advertising.
A lot of the other fan runs not on this list can be found here.
Part 5 of Bern's Platinum run has her catching (FINALLY) a male Shellos. The next scene is a Gender Flipped parody of one from Green Lantern, where Hal Jordan greets their newest recruit (a girl).
If characters named Mitch and Stella plus an abuser named Stanley aren't enough, then an obvious homage to theSkyward Scream makes it pretty clear Platinum is taking a couple cues from A Streetcar Named Desire.
Stupid Sexy Flanders: Upon seeing Juan for the first time, Hale becomes completely aware of why he has so many fangirls.
Yandere: May. This is also Deconstructed over the course of the strip as it shows why she's so psychotically possessive of Hale. She gets better.
Robotv7's Nuzlocke Challenge
Tropes seen in Robotv7's Nuzlocke Challenges:
Bittersweet Ending: His first run ends with only three Pokémon left alive, and he gets called out on the cost of his quest.
Downer Ending: His Sapphire run. By the way, since Robot quit Nuzlocke forums, the last chapter was drawn by This Guy.
Gamer Chick: Erika's all-female gym is depicted as a very snide, prideful group of these. His Pokémon defeat them by going into Sincerity Mode and paying them compliments, and the ensuing Logic Bomb makes their heads explode.
"Where Are They Now?" Epilogue: Used at the end of his first run, with the twist of making the cast out as Animated Actors. Does not appear to be canon, as seen by Brotodile's cameo in his second run. The Blue run also makes use of this trope as well, and it is every bit as hilarious and probably non-canon as the first.
Nyachan's Nuzlocke Challenges
Nyachan's Nuzlocke Challenges provide examples of:
Defeat Means Friendship: Naturally. But unlike the games or anime, it's much weirder considering Locke's Pokémon (and all Pokémon in her verse) are completely sentient and can talk. Basically, Pokémon become willing slaves if beaten up by a given trainer...
Girliness Upgrade: A temporary one for Locke and all her female Pokémon when they hit the Celadon Department Store. Promptly subverted when she ignores a sales girl offering Pokémon dolls in favor of TMs to increase her battle power.
Hammerspace: Barb is shown getting the BlackGlasses and deciding to just carry them, but they're never seen again. Same goes for all the held items.
Happily Adopted: Spuds Jr. evolves into a Togetic (which requires maximum Happiness) straight out of the egg.
Ineffectual Sympathetic Villain: Gary has shades of this. Despite the fact that he beats Locke to every gym and even beats the League before her he just never achieves his real goal, even losing his arm when he tries to capture Mewtwo. And, of course, the only reason he tried was an attempt to get strong enough to defeat Locke.
Mundane Utility: Rick the Voltorb/Electrode doubles as a music player. Each chapter he appears in also comes with "Rick's Playlist" featuring a relevant song.
Mundane Fantastic: Spuds and Barb, a large hulking plant monster, and a spiny poison mammal, working in human convenience store has shades of this. Mainly because no one seems to care or mind - until their size causes some wanton destruction
Non-Lethal K.O.: Every single time one of Locke's Pokémon KO's an opponent, with the probable exception of Gary's Raticate.
Four of Locke's Pokemon [[note: namely, her Croconaw, Geodude, Paras and Hoothoot evolve at the same time when battling a Team Rocket grunt.]] In the comments, it's noted that only two of them actually evolved at that point (the others evolved during a grinding session afterwards), and that the others were depicted evolving in that moment due to a combination of this trope and for the sake of saving some time.
Barb has one right at the beginning when she learns Double Kick.
Trolling Creator: On April 1st of 2012, Petty claims to be ending the comic because she just doesn't have time anymore. (This after her updates have been getting less and less frequent for months.) Oh Petty, you sure are a stinker.
Troubled Abuser: Silver, who is a total jerk to all his Pokémon, but obviously has some serious issues of his own, especially if, like in the games, Giovanni turns out to be his dad.
Undying Loyalty: Silver's Bayleef toward him, despite suffering emotional and verbal abuse from him, not to mention risking physical harm on his behalf.
We Hardly Knew Ye: Simon the Dewgong, who appeared and died in the Sevii Islands update. He had a grand total of one panel.
Anti-Villain: Silver, deconstructed when his methods are called out by Giovanni.
Apocalypse How: Wild Pokémon everywhere suddenly become murderously violent and begin attacking tame Pokémon and humans. Calamity ensues. At least Regional (Johto and Kanto are definitely affected), possibly Continental depending on how widespread the change is.
The Apunkalypse: Some well-known characters are completely unrecognizable for their post-apocalypse makeovers.
Art Shift: Every time Candace sees a Kimono Girl, the Girl occupies a single page drawn in a Japanese woodcut-based style. Which only enhances the creepiness.
Bunny Ears Gym Leader: Whitney tells Team Rocket that while she has a reputation as a flighty airheaded socialite, she wouldn't have been a Gym Leader in the first place if she weren't still one of the best in the business. Her people skills also serve her tremendously after the change, since she's able to make people trust her and cooperate for survival.
Due to the Dead: Candace has her first ever loss, Hellacross the Heracross, tattooed on her left shoulder.
In Blackthorn City, we get a closeup◊ (spoilers) revealing that she's similarly honored all her other dead Pokémon. (Visible tattoos, counterclockwise from top: Hellacross, Alastor the Gastly, Watchwing the Noctowl, Clutch the Exeggcute; not visible but implied: Flashpoint the Flaaffy, Crucible the Ninetales)
Dying Moment of Awesome: Jasmine evacuated her people to the Lighthouse when Olivine City flooded, but couldn't make it in herself and was swept away and drowned outside. She was the only casualty in Olivine.
In the Prologue, Elm's Cyndaquil evolved twice before she eventually succumbed to the swarm.
Egopolis: Azalea Town is renamed to Bugsy Town, in honor of its 'defender'. It gets changed back once the tyrant falls.
Eldritch Abomination: Missingno definitely fits the bill, as does the thing that ate Silver's Gengar.
The thing that ate Silver's Gengar is now known to be Lugia, which had been dormant in Candace's unconscious, and is now awakening. It also created the illusory Kimono Girls.
Even Evil Has Standards: Giovanni is more concerned with rebuilding Johto than anything else, and is not pleased with where his son's vendetta towards Candace leads.
Fastball Special: Before it evolved and became too large for it, Candace was fond of doing this with her Totodile.
Humanoid Abomination: The Kimono Girls. Eventually revealed to be a psychic projection by Lugia, channeled by Candace, which is now awakening.
Frostbite the Jynx is a milder example, since she's not so much hostile as just (deliberately) creepy. She looks like a doll with disconnected joints and a creepy perma-grin.
Human Popsicle: To what extent is unknown, but seemingly a lot of things in Mahogany Town. Including the Gym Leader.
Hypocrite: Chuck tries to run off Candace as a threat... but he completely fails to do the same for someone who was genuinely insane and dangerous, Eusine. Justified, since Chuck's info on Candace comes from the dishonest radio broadcast, and Eusine seems to have been biding his time until she arrived.
The leader of Team Rocket turns out to be massively hypocritcal, claiming that Candace must be killed because she's become something monsterous, and yet going out of his way to try and make her suffer.
Five cracked ribs, a dislocated shoulder, a sprained wrist, three severe perforations causing nerve damage along my left forearm, countless lacerations, massive blood loss, and the lingering effects of a near-fatal dose of Pokémon venom.
Only One Name: Averted. In the latest update, several characters are introduced by first and last names.
Pokémon Motif: Team Rocket's ominous warnings about Candace compare her to a Zangoose, and the scarred side of her face roughly corresponds to a Zangoose's Facial Markings. Turns out their boss Silver has the code name "Seviper", Zangoose's biological enemy. Candace eventually adopts "Zangoose" as a nickname.
Power Born of Madness: The changed Pokémon are not only violently aggressive, but tremendously more dangerous. Pryce's Dewgong flash-froze all of Mahogany Town when he lost control.
Candace also has some of this... enough to bare-handedly strangle a Weavile.
Reasonable Authority Figure: Most of the remaining Gym Leaders seem to be reasonable, with the obvious exception of Lord Bugsy. Surprisingly, Giovanni is also pretty reasonable once he wises up to Silver's vendetta.
She Who Fights Monster Pokémon: Candace is arguably as wild as the changed-over Pokémon by now, including killing Seviper's Weavile with her bare hands.
Silver's hatred of her makes him cold, calculating and uncaring about who else gets hurt in the course of his revenge upon her.
Story And Gameplay Segregation: The storyline of the comic differs tremendously from the actual gameplay of the Soul Silver game. Word of God is that cutscenes involving Ethan are awkward to play, since Ethan died with New Bark Town in the comic's storyline.
Word of God also says the author lost their notes on what happened in game a while back. No one would have noticed had it not been pointed out.
Time Skip: Every time Candace takes an attack that seems like it should kill her, the storyline skips a couple of months while she recovers. As of Blackthorn City, three or four years have passed since the change happened.
Unknown Rival: As much of a Jerkass the rival is, Candace is more concerned with how his Chikorita fled from New Bark. Compared to that (and the whole Apocalypse thing), he's hardly worth her time. Until he takes over Team Rocket.
What the Hell, Hero?: Candace gives several, but the first is to Elm's Chikorita, who fled instead of trying to defend New Bark.
Candace also gets a few. Her siccing of Death Star on Jasmine Tower earns her one from Preston, for example.
Giovanni himself gets in on this when he calls out his own son, whose personal vendetta leads to the deaths of many of their men.
You Will Be Assimilated: This is a major part of Missingno's schtick, as it turns out. It gains parts and abilities from eating them whole- as in the case of Candace's Noctowl or Eusine's Electrode- or even just parts of them. Poor Beelzebub.
Kynim's Nuzlocke Runs
Tropes seen in Kynim's Nuzlocke Runs:
Abusive Parents: Bianca's dad, who is misogynist and emotionally abusive to Bianca, and mentioned to be physically abusive to her mother. Upon hearing about the latter, Elesa escorts Bianca to the police station to report him to Social Services.
Broken Ace: However, Nina feels immense amounts of pressure to live up to and surpass her parents, causing her to foster a lot of resentment towards her mother. Making this worse is how she's grown used to having her issues dismissed as 'not real problems' and coping with others' jealousy of her position.
A Day in the Limelight: Quite a few Pokemon and recurring characters get an "Extra" comic that details their backstories.
Anthropomorphic Personification: Kynim goes a different route than the games by having Reshiram and Zekrom become the personifications of the immense desire to seek truth and ideals from the twin kings.
Art Evolution: Compare the first Diamond Run issue with the most recent White Run issue and the progress is astounding.
Bilingual Bonus: Both Jojo and Rex are Hispanic and frequently utter phrases in Spanish.
The restaurant that N takes Nina to is named "The L'Navire" - French for The Ship.
Both Sides Have a Point: The explanations made for and against Pokemon battles in 036 and 037 both have legitimate points and give a deeper insight into the comic's universe.
The Casanova: Maximus, the Murkrow from Kynim's Diamond run. He immediately attracts Regina, Mel, and Annie when he appears.
Cerebus Syndrome: The Diamond run is mostly comedic, and what angst there is tends to come from someone dying. The White run is much more dramatic, with a lot of character-driven angst as well as mourning over Pokémon deaths.
Characterization Marches On: N is initially depicted as creepy, twitchy and unpredictable. But over time, he is shown to be more - for lack of a better word - normal, though is still quite awkward and prone to getting worked up.
Chaste Hero: Zach, initially. Though it seems he is gradually outgrowing his naivety with evolution.
Creator Cameo: Kynim the artist has shown up as several characters in the comics.
Deus Exit Machina: Not mentioned, but an extra comic mentions Kynim is still residing in the Sinnoh region, which would explain why she isn't there to help Alder and the Gym Leaders with Team Plasma in Unova despite their presence to the region and the potential threat they are to her daughter.
Due to the Dead: Both heroines always make it a point to give the Pokemon they have lost a proper burial.
Fallen Heroes: Several art pieces and the story implies that the that the reign of the twin kings didn't just end with region-wide destruction.
Foreshadowing: During the White run, Nina has just rung the bell on Celestial Tower and is experiencing a moment of peace with her fallen Pokemon. Lin, a psychic who serves as her guide, reaches out a hand to see if Nina is alright and is struck with a vision of Nina seemingly broken, with the shadowy figure of a Hydreigon looming behind her.
Interspecies Romance: Amongst Nina's Pokémon, Laila the Petilil/Lilligant is totally dere for Zach the Dewott/Samurott, Jojo the Darumaka/Darmanitan and Rex/Rey the Sandile are pretty flirty Childhood Friends, and Jordan the Bliztle/Zebstrika has a soft spot for sweet Mimi, a Woobat/Swoobat.
Legendary in the Sequel: Downplayed, but Kynim from the Diamond comic is well-known in the White comic, much to Nina's annoyance.
Letters 2 Numbers/Leet Lingo: Used frequently throughout the Diamond Run, especially by Haisinote Justified in that she was working with a much smaller space at the time. Completely absent in the White Run.
Magical Eye: N has these after obtaining the Light Stone.
And in the Diamond run, Gohan and Shakti were totally not an item, according to the artist's notes on the omake comic featuring them. Tyrus's affections for Annie, however, were eventually reciprocated, as were Kynim's for Roark (big time!).
Stalker with a Crush: Lucas in the Diamond run, for Kynim. "How do you know my clothing sizes?!" Eventually Haisi hooks up with Lucas instead.
In the White Run, the role is given to N who has developed a crush on Nina but doesn't know how to express it. Lampshaded in the credits, where he's billed as "Creepy Stalker", and in the Valentine's Day omake:
Roses are red, Violets are blue. If a stalker asks you out, What do you do?
Byron's misogyny is played for laughs in the Diamond run, especially once Kynim gives him a taste of his own medicine and orders him to make her a sandwich after the fight.
Stealth Pun: Bianca speaks and behaves like she's from the Deep South, especially in the beginning. She's a SouthernBel.
Sticky Fingers: Pierre, Cheren's Liepard. Someone mentions that he's pickpocketing trainers, he steals Nina's bag, and attempts to steal Laila's Miracle Seed... only to Laila to hit him with a Magical Leaf.
Stun Guns: The Shadow Triad have electric kali sticks, which they use on Nina.
Talk to the Fist: How both Kynim and Nina often respond to all the nonsense around them.
"Where Are They Now" Extra: Several of the Extra comics tend to give information on the characters from the Diamond Nuzlocke. Most notably, Haisi and Lucas are married and adopted a child, with their jobs as Frontier Head and Researcher respectively.
Attack of the 50-Foot Whatever: Jormundgar's closer to 80 feet, actually, fitting her namesake, but all of Nessa's Pokémon are way bigger than the pokedex entries for them. All of them except Thorn (a Lairon) are taller than Nessa, who is herself not particularly short at 5'11". In Jory's case, it's a bit of a problem— because of her size, she's rarely let out of her pokeball.
Thorn eventually becomes an Aggron of Kaiju-esque stature.
Hidden Agenda Villain: Not just the villains, either. Scott seems to be leading some sort of operation requiring the cooperation of Steven Stone, all the Gym Leaders, May, and Nessa as an Unwitting Pawn.
Jerk Ass: Fenrir was not very friendly at first. He eventually mellows out... a little.
Magikarp Power: Fenrir was partnered with Jormundgar the Magikarp so he'd get a taste of this and learn not to bully other Pokémon. By the time Jory evolved, he'd bullied her into an Unstoppable Rage, and the lesson almost killed him.
Vocal Dissonance: Thorn as a tiny wild Aron used his thundering voice to frighten others away from sections of the cave that seemed likely to collapse. He also sings. After evolving, his appearance is more appropriate for his voice.
Jerk with a Heart of Gold: Ken is kind of a douche at the beginning of the run, giving his pokemon suggestive names and constantly making gay jokes at Gary's expense, but he gradually matures as the run progresses.
The Killer In Me: The source of Ken's Axe Crazy tendencies, of the Amnesiac variation. How he became this way is still unknown, even to Ken.
Laser-Guided Amnesia: Ken strangely cannot recall why Daisy and Gary treat him so coldly and has no recollection of the several months before the events of the story.
Lovable Sex Maniac: Getting into Daisy's pants was his initial motivation for becoming champion.
Mysterious Past: Ken seems to have had some sort of interaction with Team Rocket and/or Mew. It seems like even Daisy and Gary have this as well.
Baleful Polymorph: The Pokémaniac is accidentally transformed into a Clefairy, as per the standard game plot, but is not transformed back into a human. He ends up pretending to be an ordinary Clefairy and joining Team Kick@$$ rather than admitting to being the man in the embarrassing photos which Ken finds on his computer.
A Million Is a Statistic: Manic appears noticeably less emotionally affected by his early deaths in Final Vega than he has been by previous deaths in other runs. Subverted after he is shown the reality of his situation.
Abusive Parents: In Derpy Emerald, Manic's mother is a prostitute and his father is an absentee; she is later redeemed. In Spirit Electrum, Peace!Manic's mother is an abusive drunk (in stark contrast to War!Manic's mother, who is loving and kind).
Also, Bianca's father in Paint It Black, though he comes to realize what he's become and promises to seek help when confronted by Elesa, Manic, and Bianca.
Alternate Timeline: Brought up in Spirit Electrum, where, in one of the universes, there never was a Manic that defeated Gary Oak and Mewtwo in Infernal Red, meaning that there was no power vacuum for Genwyn to occupy and start the war against Johto. The Manics from the "War" world and the "Peace" world swap back and forth between the timelines whenever they enter a new town for the first time, or when one of their Pokemon dies.
Remember the Slugma that Mike knocked out in Infernal Red on the Sevii Islands? Der Gnizalb happens in a timeline where this never happened, which resulted in the Slugma's power growing exponentially, as it had no natural predators, and eventually Slugma ascended to godhood. This resulted in the events preceding Der Gnizalb.
Ass Kicks You: There's a scene in Infernal Red, in which Gary's Blastoise taunts Creosote (Snorlax) with the classic "Are you going to sit on me?" line. Creosote does just that. And gains a level doing it.
Baleful Polymorph: The trainers who previously failed to beat the game in Infernal Red turn up as wild Pokemon afterwards.
In Dark Stars, Manic himself even qualifies.
Berserk Button: For Manic in Spirit Electrum, trying to harm or forcibly weaponize Grant, or generally separating him from Manic.
Big Bad: Each run has its own. Derpy Emerald has Wallace, Infernal Red has Mewtwo, My Little Pokemon: Friendship is Super-Effective has the spirit of Wallace, Fatal Platinum has Cynthia, Paint It Black has Ghetsis, and Spirit Electrum has Red/Genwyn. Only after all five runs was the Big Bad finally revealed to be Wallace and Darkrai as a team.
Bilingual Bonus: Gustav from Derpy Emerald and Frieda from Paint It Black both invoke this; if you happen to speak Spanish or French (or are willing to play with a translator), you'll get more out of their dialogue.
Final Vega is, much of the time, one big version of this.
Big Damn Heroes: In Dark Stars, Sophie battles Maylene. Against her final Pokemon, Cyrano is about to get killed by Counter, but then a fully-evolved Manic returns to the party to block the hit. He promptly takes down the Lucario via Close Combat.
Bittersweet Ending: Final Vega. In the final gameplay update, Manic's team successfully defeats Darkrai's team. However, the cost is high: the shade of Alder's Volcarona scores a critical Overheat on Yuki. She dies instantly.
Blessed with Suck: Being an Oracle may grant you near-omniscence, but they are still cursed with an inherently high chance of being killed eventually due to being specifically targeted by the Big Bad.
Break the Cutie: In Blinding Light, Max starts out as an upbeat, friendly, enthusiastic puppy. Then he is taught to kill, and forced to do so repeatedly despite his misgivings.
Chekhov's Gun: Found in My Little Pokemon: Friendship is Super-Effective. Rarity's special Pokemon Power appears, at first glance, to be Run Away as an additional ability. Considering how rarely the actual ability is used in the games, it appears to be useless... until it saves everyone's lives.
Another one that thankfully didn't have to be fired in Fatal Platinum; the last move that Franklin the Lopunny learned before asking to be retired from active duty was Healing Wish, which basically acts as a Full Restore on another party member in exchange for KOing the user. In the event that Manic ran out of time, Franklin would have used Healing Wish, sacrificing his life to give Manic one last day to finish his quest.
Creepy Child: In Spirit Electrum's peace world, Joey is just another kid. In the war world, he's an allied agent and skilled sniper who is revealed to be following Manic around with orders to take him out if his behavior becomes too erratic.
Curb-Stomp Battle: Near the end of Paint It Black, Arthur enters the battle with N, having stated that it is his dream to defeat N's legendary dragon. Most major plot battles involve switching; not this one. Arthur stands there and defeats N's entire team single-handedly. Immediately afterwards, the same happens to Ghetsis' team; different pokemon, same result.
In DONUT'S ATOMIC KITTEN SLEDGE, Underwear solos the entirety of the Elite Four and then turns to being transport and backup for the remainder of the run.
Dark World: Manic's take on the Gen II remakes has him play both versions at once, switching perspectives every time he enters a town. He incorporates this into the story by building two designations for them, though it's never clear which is worse: Soul Silver, with its peaceful world and unpleasant NPCs, or Heart Gold with its war-torn environment but kinder NPCs.
Dangerously Genre Savvy: Varas, Manic's rival in Spirit Electrum, knows... well... everything. He knows about all the different runs, he knows who the ultimate Big Bad is (and is, in fact, employed by him), and he understands that nothing that is happening is real; in fact, his stated goal is to win existence independent of the game world by destroying Manic. The fact that he blames Infernal Red's Manic for murdering his parents is just added incentive.
Deader than Dead: Reflected upon when Jonas dies in Paint It Black. In a previous run, Dana had been reincarnated by Mew as repayment for services rendered. Here, Manic recalls that the local legendary Pokemon do not have that sort of power, and that any pokemon he loses is permanently gone.
Did You Just Punch Out Cthulhu?: Invoked: another consistent rule of his runs is that in order for him to win, he needs to have defeated all one-time encounter Pokemon or face failure. Spirit Electrum exploits Loophole Abuse by catching Lugia, using it in his team, then having it be a casualty in the last battle of the run.
It's actually all legendary pokemon, not all one-time encounter pokemon. This is used to justify not fighting Slugma at the end of Der Gnizalb, which is a one-time encounter but not a legendary pokemon.
Exact Words: Darkrai. While being consumed, Wallace complains that there was a deal. Darkrai replies, "THE DEAL WAS THAT I WOULD DISPOSE OF MANIC - AND I SHALL - AND IN RETURN, YOU WOULD FEED ME. AND YOU ARE. NO TERMS HAVE BEEN VIOLATED." The deal never included Wallace's survival.
In Blinding Light, the prophecy states that Zekrom awaits a hero. The hero is Max, not Vile - it never said what species the hero had to be.
Fantastic Racism: Exemplified by Genwyn, who is revealed in Paint It Black to despise all non-Kanto Pokemon.
Flat "What.": Manic's reaction to seeing the starter Pokemon in Final Vega.
Also his reaction to Proton saying he's the scariest and cruelest guy in Team Rocket.
Freak Out!: Manic in Derpy Emerald didn't take well he was infected with a condition that can cause his Pokemon to die if it faints.
Groin Attack: In Blinding Light, Vile has Zerzan "geld" Clay as his punishment.
Guardian Entity: Manic's Oracles, made to guide Manic through his quests and explain how to undo their circumstances.
Explained by Vile in the Q&A: "He has no mouth, buffoon."
Heroic Sacrifice: In Infernal Red, Trevor shoves Susan away from an exploding Koffing and takes the blast instead in order to prevent her from being killed in front of her daughter, Lacey. The sacrifice saves Susan and helps Randy to come to terms with his situation.
He's Back: Manic returns to the team in chapter 15 of Dark Stars.
His Name Is...: In Der Gnizalb, the last words of Matilda. "Pay attention to what's...to come...this is what...it is...to..."
Played for Laughs in the Donut run, in the scene where Susan returns from the dead temporarily as a ghost to tell Donut to teach Surf to Underwear. When leaving the mortal plane, she happily exclaims "Hey, there's my..." No points for guessing what it is.
Jerkass: Anemoi the Lugia from Spirit Electrum. Until shortly before his demise, Jacob from Paint It Black. Iwao from Final Vega. Fenrir from Der Gnizalb, recently outdone by Beat.
Boris from Paint it Black is enough of one that it gets him removed from the team.
Keet: Max from Blinding Light, up until he evolves into a Stoutland.
Killer Rabbit: Franklin the Lopunny in Fatal Platinum pulls his own weight repeatedly in battles.
Language Barrier: A great big one in Final Vega. Japanese appears to be the local language. Most of the game text is in Japanese. The NPCs speak it. The Pokemon speak it. Whether we're talking about the protagonist or the player, Manic... doesn't. Being overcome, little by little. Manic eventually learns some Japanese via total immersion in the language for over a month, giving him enough knowledge to understand his pokemon but not enough to understand NPCs.
Lethal Joke Character: Quite a few. Ace from Derpy Emerald, Bela the Murkrow from Infernal Red, Applejack from My Little Pokemon: Friendship is Super-Effective, Roxanne from Fatal Platinum, and Dawn from Paint It Black. Exemplified with Roxanne, a Bibarel so utterly unstoppable that sheliterally pulls herself out of the PC box, rips through several doors to reach Flint, Manic, and the rest of the team, and informs the dying hero that she'll end him right then and there if Nero is dead. Oh and let's not forget Bump the adorable man-child Swalot who will murder your face off if Manic tells him you're a bad person.
Literal Split Personality: Each run in the Manic Saga gets its own distinct Manic. Derpy Emerald gets the original. After the run ends, each region gets its own aspect of Manic:
Kanto gets Manic, Self-Aware, to embody his knowledge of self and the fourth wall.
Hoenn gets Manic, Innocent, to embody his naivete.
Sinnoh gets Manic, Courageous, to embody his fearlessness.
Unova gets Manic, Experienced, to embody what he has learned.
Johto gets Manic, Determined, to embody his refusal to give up.
The saga ends with Manic, Ascendant, who is the result of combining six runs' worth of experience into one mind, who goes through the aptly named Final Vega.
Nintendo Hard: Packed with overpowered gym battles, difficult puzzles, and even some outright cheating, Manic's run of Vega is this. By the time he finishes the run, far more pokemon have died than in any of his previous runs.
Nostalgia Filter: Genwyn and its followers are a reference to this, since they enforce inherent superiority in Kanto Pokemon over all others, and to hunt down and kill Manic at the same time.
One of Us: Manic, Self-Aware (from Infernal Red) has stated that he "knows the tropes", even using some tropes by name in Spirit Electrum's finale.
One Linoone Limit: Utterly subverted in Spirit Electrum, where Manic notes that the rules give him the opportunity to ignore duplicate pokemon, not the obligation. He then expends time and resources gathering as many Linoones as he can to abuse Pickup. His effort is a failure, though; not a single one of the Linoones caught in this way has that ability... except for Trish.
The Plague: The Nuzlocke is depicted as a disease with many variants in this setting, with Manic from Fatal Platinum getting a Degenerative Necrotic variant and Alder getting an infectious variant.
Sadistic Choice: Straight through the fourth wall near the end of Spirit Electrum. After Manic beats Lance in a rematch, a vortex opens that acts as a joining point between the two worlds, just like the first time. The difference is that the first victory allowed Manic to shift as many pokemon between worlds as he chose. This time, Manic is forced to choose which world is allowed to survive and which one vanishes forever. The viewers are first shown the two possibilities where the War world is chosen and War!Manic commits suicide because he lost Grant, and where the Peace world is chosen and Peace!Manic becomes too preoccupied with the Champion's duties to carry on his quest. Eventually both Manics decide to Take a Third Optionso that the two worlds are combined into a single world.
Dark Stars has one before the first gym, where Sugar the Smoochum can only stay on the team in exchange for the retirement of Gavin, Cyrano, Melita and Lewis. Of course Sugar gets the box in the end.
Sequel Hook: There's one at the epilogue of Final Vega.
Shout-Out: The first gym battle in Paint It Black is an Epic Rap Battle (though not so much 'Of History').
One could also consider the entirety of the My Little Pokemon: Friendship is Super-Effective run to be a Shout-Out, as it contains a crossover between the Pokemon universe and the My Little Pony: Friendship Is Magic universe (as alluded to in the title).
10-Minute Retirement: Occurs in Paint It Black, when Jonas is killed. Already in a vulnerable state after the recent death of Jacob, Manic is informed that it's within her power to stop any more of her friends from dying, that all she has to do is quit and go home. After a Heroic BSOD, she does precisely that. A Rousing Speech delivered by some old friends is required to snap her out of it, and when she does, she hits the ground running.
Villainous Legacy: The entire second Manic saga. Manic is forced to contend with a version of each region that has had its timeline warped by Darkrai, despite its defeat. Why? Because until he fixes the timelines, none of his friends can go home without being instantly eradicated.
Villainous Valour: In Blinding Light, during the battle with N, Max remarks that - among Vile, N, Ghetsis, and Alder - none of them have goals that are good for Unova. After Ghetsis is killed by Zerzan, N decides that Max is right...and transforms a supposedly innocent handshake into a last-ditch effort to help Unova.
We Cannot Go On Without You: A consistent rule in Manic's runs are that starters cannot leave the party, and if they are killed, he loses the run immediately.
Wham Episode His Derpy Emerald run gets a bit more serious when Flannery freaks out and has her Torkoal attack Manic directly.
Also part thirteen of Dark Stars, "Farewell Tour."
Wham Line: Found in Infernal Red. "Professor Oak is dead."
Also found in Dark Stars. Manic has left the party.
Word Salad Title: The Donut runs have these and seem to change with every update.
Demonic Possession: Glitch!Ara possesses multiple people over the course of the Black run in order to kill normal Ara, including N.
Enemy Without: The Big Bad for the Black run, the "Glitch", is the embodiment of Ara's Survivors Guilt over the deaths in his challenges. It usually possesses NPC Trainers (including N) and Pokemon, but it shows up for the final battle in the form of his Pearl run's female self.
...and deals the last blow against Cynthia's Garchomp, as well.
Ara likes Bug-types in the Pearl version run. Clutterbug the Trash Cloak Wormadam was beloved for her sole weakness being the rarest type in Sinnoh, and Chopin the Kricketune went to the Elite Four with the rest after Clutterbug became a casualty of Cyrus.
Mind Screw: There's not much sense to be made of how Ara's female form managed to gain an entity of its own and gain reality-warping powers. Nor is there much sense in how male!Ara managed to do the same near the end.
Shrinking Violet: Soleil the Scraggy/Scrafty, who spends most of her time hiding in her shed-skin-clothes. Ara says he was tired of the "aloof gangster" archetype. After Nineveh's death, Soleil grows out of her shyness and becomes a Heartbroken Badass.
Who Names Their Kid Shini?: Wondered by Shini himself at the beginning of the comic, again after he becomes James, and yet again every time someone addresses him by it. Chuck indicates that Shini named himself that.
Wrap It Up: After canceling the comic, the artist decided to do a series of written summaries to explain how the plot would have progressed if he finished.
Adorkable: Bill is described with exactly this word.
All-Natural Snake Oil: Cianwood Secret Potion is apparently made with all natural ingredients. But, as Mike internally notes, 'Hemlock is natural. So are bears.' The lighthouse Ampharos effectively receives a Hideous Hangover Cure.
Blatant Lies: Mike protests that he wasn't scared of flying on Kate's back, merely 'startled'.
Kate:If by that you mean you clasped your arms around my chest, screamed like a girl all the way back and swore to never fly on anything more unprotected than a passenger plane, then yeah. You were pretty 'startled'.
Can Not Spit It Out: Silver's Quilava Lee spends a long time dancing around the fact that he has a huge crush on Kate, getting tongue-tied and embarrassed merely from being around her. It is entirely unrequited on Kate's part.
Catch Phrase: Gamma's repeated use of the word 'fascinating'. It even describes its own death in such a way.
Fan Disillusionment/ Broken Pedestal: When Mike first meets Lance at the Lake Of Rage, he idolises him as one of the strongest Trainers in all of Johto (even thought he doesn't know about his job as Champion). Then after repeated instances of him acting like a jerk during the Hideout infiltration (particularly when he 'saw how well you were doing (against all the Grunts and the Admins) that I hung back'), he comes to realise that Lance is actually kind of a dick in reality.
Felony Misdemeanor: Bill refers to Colin sleeping on his keyboard while he was working "as if it was the eighth cardinal sin".
Fourth Wall Observer: Harry the Sudowoodo. He was originally from a different series by the same author and was dragged over to this series as a punishment for breaking the Fourth Wall too much in that work, which should say everything.
From Bad to Worse: From getting lost in Dark Cave to getting lost in Mt. Mortar, and then getting lost in the Whirl Islands.
Gentleman and a Scholar: Clyde. Polite and respectful, speaks with class, acts with gentlemanly etiquette, issues full challenges even when grinding against wild Pokemon and frequently comes to conflict with more self-serving loutish types (particularly Team Rocket, and Colin).
Jerkass: Colin, of the 'insufferable' variety. Condescending and aggravating, he only gets away with not being throttled because the team, as much as they hate to admit it, need the advantages he brings.
Killed Mid-Attack: Sammy. Just before he launched a huge Razor Leaf volley, Jasmine's Steelix used Iron Tail and killed him instantly.
The Lad-ette: Kate the Spearow. She even threatens to peck Mike in the face on occasion.
Mood Whiplash: About as jarring a one as you can get - from Chapter 5.5, a cheerful Lonely Island parody about Mike's Pokemon blowing all his money in Goldenrod City, to Chapter 6, in which four named characters die.
Multiple Head Case: After Solenoid evolves into Magneton. Its sentences get passed around its three heads at random intervals, sometimes doing a full lap in one speech.
My Greatest Failure: The series author believes that his run of Goldenrod City Gym in which four Pokemon died, three of them to the same opponent, is probably the biggest failure ever recorded in a Nuzlocke run that didn't wipe out the entire party.
"Not Making This Up" Disclaimer: When particularly stupid/silly lines are quoted from the game (not to mention the part where, in the game, instead of using Fly Lance literally spirals into the sky and disappears), the author tends to put in a short disclaimer to say that this is a genuine thing from the game.
One of the titles Harry makes up about himself is 'Hanger of Lampshades'.
OOC Is Serious Business: The disaster in Chapter 6 was so bad that the Author apparently forgot his usual Nuzlocke recommendation in the artist's description.
When Colin is being quiet and no-one tells Harry to stop breaking the Fourth Wall, you know they're upset about Lisa's death.
Ow, My Body Part!: When Mike falls into Ruins of Alph the first time, he tells the researcher 'I think I bruised my appendix'. The second time, it's his coccyx. When he falls through the floor of Olivine Lighthouse, he cries 'Ow, my fovea!'.
Several of the In Which a Trope Is Described lines at the start of chapters, including 'The Cold Light of Mourning', 'For Whom the Doorbell Tolls' and 'Overexposure to Gamma Radiation' (Gamma is the name of the Unown that took Bugsy's Gym down so fast it wasn't even worth showing it in the story).
Puppy-Dog Eyes: Colin tries these on his first appearance, but they aren't very effective. Amy's are super effective.
Rage Against the Author: Downplayed version: Rather than being angry, Harry makes continual jokes at the author's expense.
...Then I played through this section of the game and both Mike and I realised that actually Lance is kind of a dick. No two ways about it. He's a dick. And we've already got Colin for that, so there's only room for one dick in this series, and I should stop before I say something really awkward.
Small Name, Big Ego: Morty. Even when he tells Mike 'may the best man find the Legendary first', he still mentally adds 'which will clearly be me'.
Solenoid as well, although not as much. More Literal-Minded - when asked 'Anything else about yourself you'd like to say?', he answers 'Yes' and then doesn't say anything else about it until specifically asked again.
Ambiguous Gender: A few protagonists are this, but it is widely used in Para's Nuzlocke to the point where one of the most asked questions of the author is "What is Para's gender?"
Bittersweet Ending: Kai's run ends with all her Pokémon apparently alive. They leave her while she sleeps, noting that it would be too dangerous for her to follow them. It ends as a Shout-Out to Inception.
Can trainers understand what their Pokémon are saying? If so, how? Can only some of their Pokémon communicate with them, via human speech or telepathy, or can all of them speak freely?
Naming is variable. Is it just a nickname, or do wild Pokemon have no name at all? Does the new name override their previous one? Are they human-like names, or, well, not? Kindle-flower's run suggested that wild Pokemon do have names, but they don't translate well into human languages so they just let their trainer give them a name they can reasonably use.
The scale of the region is pretty much variable. To take Johto as an example, in some stories Violet City is a day and half's walk from New Bark Town whereas in others Mr. Pokemon's house is a matter of hours away from Goldenrod City.
Fake Kill Scare: Used often enough to be considered another unspoken tradition.
Green Thumb: It's common for Red/Blue/Fire Red/Leaf Green Nuzlockers to choose Bulbasaur as their starter. In the comic, it may be justified as the character thinking it's cute or favoring grass types in general, but strategically speaking, it is the best to start with when you want to make a run with as few casualties as possible, since it has a type advantage against the first two gyms. And its Poison typing gives it an immunity to poisoning.
Subverted in Gold/Silver/Crystal/HG/SS runs. You'll be hard-pressed to find a Nuzlocke that has a player choosing Chikorita. The poor grass type has a type disadvantage against BOTH the first two gyms. Really, if you counted, Cyndaquil is by-and-large the most popular starter for Johto with Totodile as a close second. Ruby/Sapphire/Emerald nuzlockers usually prefer Torchic and Mudkip (the latter for its memetic status). However, the aversion to grass types isn't as egregious in Gen 3 as it is in Johto.
In Petey's run, every Gym Leader got one of these.
Left Hanging: A lot of Nuzlockes are abandoned for various reasons, though a lot of artists who do this simply admit that it's pure laziness.
Lonely at the Top: A lot of trainers end up feeling disillusioned, miserable and guilt ridden because of all the deaths that they are indirectly responsible for. Sometimes remedied with a You Are Not Alone moment from their Pokémon.
Love Hurts: For Arceus's sake, don't ship in a Nuzlocke comic! As it will happen very often. Through there's a few exception. Most notably Barb and Spuds.
Heck, it hurts for humans as well. There's one Nuzlocke comic where Cheren is in love with Bianca... But not only is she a lesbian, but she's dating Elesa. And he didn't know these two things until a bit after he lost to Elesa. Needless to say, it hurt for both sides.
One Pidgey Limit: Some comics will have a "Dupe Clause" in the rules, which will allow them to catch another Pokémon on the route if they already have one from a previous route. For plot and gameplay purposes, it makes sense to not have three or four of the same Pokémon.
Only Sane Man: A lot of Nuzlockes that put comedic focus on the Fridge Logic and character interpretation have a habit of making the protagonist come off as this.
Running Gag: Across multiple Nuzlocke's even. For whatever reason, pretty much every Platinum run has the main character explicitly avoiding the plot dialog with Cyrus in Mt. Coronet.
"PCHOOOOO" seems to be a popular onomatopoeia for pokeballs.
Schedule Slip: It's been pointed out that the gap between comic updates tends to slow down as the Nuzlocker nears the end. It can probably be chalked up to the final strips being longer, better drawn, and overall fatigue from doing so many comics.
Taking You with Me: Selfdestruct/Explosion, the bane of every Nuzlocker's career. Also sometimes a Heroic Sacrifice, like in Petty's Nuzlocke above. There are also times where a Pokémon will die from poison or recoil after killing off a harsh enemy, as in Wasserbienchen's In Black And White with her Herdier or Marriland's first Nuzlocke and Tentacool.
Wham Line: From Kotone's Nuzlocke adventure Earlier today... I died, didn't I?
What the Hell, Hero?: Expect this to come up a lot, especially if the concept of the Nuzlocke is a plot point, since in most of them, the hero will get called out for allowing his Pokemon to die, often in preventable situations. Especially when it's a Black and White run and the person doing the calling out is N.