Continuing Is Painful - Characters can die in the line of duty, and they can be resurrected. However, it costs a ridiculous amount of money, and if the character can't pay it, he/she might find him/herself indentured to a Councilor or a corporate executive who paid the fee. An exception is made for characters killed by another member of Confuto Ordinatio - in that case, the killer pays the fee or is indentured to the person who pays - but only if they get caught. This also doesn't apply to characters from Aware Worlds — they need to have the money available up front, which is why High Councilor Statham hasn't been rezzed yet.
Tewi Inaba not only having her good luck negated, but being given cripplingly bad luck.
Rider also found that a good way to keep Omi in line was by threatening to tell Sakura that he's been reckless or otherwise misbehaving.
Corrupt Corporate Executive - Several have been popping up now that the game has had playable characters killed and resurrected, trying to coerce them into working off their debts doing less than ideal jobs with high odds of being killed again (thus their indentured servitude continuing even longer). The exception is Devorah Kebi, CEO of Gilded Comet, who is most certainly NOT corrupt.
Enemy Civil War - Both of the enemy organizations so far are in a constant state of this. [Humanity] suffers from infighting among various factions, and the Children of Entropy are so disorganized that they need protective fields around their bunks to protect them from sneak attacks in their sleep.
Felony Misdemeanor - Sasami has gone to great lengths to hide the fact that she and Tsunami are bonded, mostly because she's an Agent and Tsunami's a Councilor. However, the people she's told - by her own volition, by force or by accident just... don't care. Granted, she's an eight-year-old with severe self-esteem issues concerning that, so...
Hive Mind - Every version of Chief Enforcer Morrison is connected via psychic link. Ivan learned this initially by using Mind Read on him. The result overloaded his brain and put him in the hospital wing.
Huge Guy, Tiny Girl - Shizune is deaf, and since the translation function on the PDAs only works for spoken language, she needs an interpreter. She gets one in Naoki, a ten-foot-tall oni. The two are seldom seen apart.
Although there have been bills to introduce uniforms.
Mister Muffykins - Schnookums the cat is an irregular NPC who escapes from his overbearing owner. Agents are usually tasked to take him back, usually feeling guilty. Come on, the poor kitty got dyed GREEN for St. Patrick's Day.
Mood Whiplash - The game is generally lighthearted, but there are jobs where shit gets real. During the first major event, the agents investigated the disappearance of the Persona 3/Persona 4'' world. Serious jobs of lesser magnitude have occurred, too, such as dealing with renegade Espers powered up with GN Drives.
Taken to its most extreme during the OS update event. It started out with silly malfunctions for wacky hijinks, then BAM — virus hits, everything shuts down, and evil twins are roaming the compound and abducting people.
And then, of course, was the Aethr integration event. The mods had already said that this would be a major event, so it was obvious that the 'happy' parties wouldn't stay happy.
Let's not forget the Kyons. Kyon often recognizes people from different canons and even did research on them after the Man In Red tried to take control of Haruhi's powers. Kyonko, on the other hand, will actually argue with her player in her monologues and comment on the game's format when the other player forgets.
Kazumi Hagino was a big offender of this trope during her early months in CO, blatantly breaking the 4th wall by recognizing (and even verbally saying she recognized) people from the games she played. However, her ability to break the fourth wall has recently taken a huge hit from the Nerf bat.
Non-Player Character - Several Councilors and Senior Councilors were introduced for the first major event, as well as Chief Enforcer Morrison, CEO Devorah Kebi, and the occasional other staff member.
Noodle Incident - Not planned as such, but how precisely doesGuybrush Threepwood best Evangeline A.K. McDowell? All that's known is she broke nothing important, and apparently he flat-out humiliated her enough to make her write a letter of apology for the incident in question (she still balked at calling him a "mighty pirate").
Original Generation - There are quite a few OCs, including the OC world Earth-YT ("Yakuza Theatre") and OC World Earth-NCaHN ("No Chance at High Noon").
Kyonko's clone is a more literal version of this, having been born during the Mainframe Crash event then becoming a player character due to her popularity among the playerbase after her mind gets downloaded into a different body.
Morrison was recently revealed to be one of these as well, saying he never had another world to call home but Confuto Ordinatio.
Our Elves Are Different - The NPC Elves are high magical, long-lived, and arrogant - they're also disdainful of worlds that have religion that doesn't manifest Physical Gods and can't be argued with.
Ramming Always Works - Sasami decides to ram the Children of Entropy's main battleship with the ship form of Tsunami to save the other battleships and mecha from its main cannon. It works, but for her troubles, it leaves her drained and shot at.
And then they get their original Souji back, as well as a Minato.
Baron Archibald Von Strauss exists due to Kyon's player desperately needing an in-character reason for him to stay in Confuto Ordinatio after Mikuru dropped and requesting a subplot.
Kyoko's player originally intended to either let her die or be transferred to another branch, but when the other players expressed their love of her, she decided to keep her around and officially app her into the game.
Lucia thinks everyone (especially Matsu) is a pervert.
World-P3/4 being constantly threatened by terrorist organizations and eldritch beings.
Screw the Rules, I'm Doing What's Right: Ksthellixis, of all people, decided to say "screw it" to the red tape for once in his life and run in unbidden leading the cavalry to help out during the Aethr plot.
Time Crash - The result of Guybrush breaking a magical voodoo clock. The gates to other worlds were thrown into flux, characters were aged up or down, some characters got either sped up or slowed down, some characters regained items that should not exist in the present (such as Phoenix receiving Dahlia's locket or Ragna receiving his severed arm), and multiple versions of characters appeared at the same time.
Weaksauce Weakness - Terrus has a bomb strapped to his neck to keep him in line. Unfortunately for him, the makers didn't bother making it resistant to external stimuli...like an electrically-charged blade.
Wham Episode - And how. After an episode of the CO branch having to organize to host discussions on whether the world of Aethr would be synchronized to CO. After the bill passed, there were wonderful parties... and then Nyarlathotep set off bombs alongside a new interdimensional terrorist faction, the Children of Entropy, which doomed the world to a horrific extinction in a matter of weeks and spread a horrific taint across it... All to create the Shining Trapezohedron, full of things mankind was not meant to know and capable of bringing despair to God-knows-how-many worlds.
Aid efforts started immediately. Unfortunately, soon after the taint started taking effect, all abilities not of self-originated power began to be corrupted. Like, say, Bolverk, the seal that keeps Noel Vermilion's repressed hatred in check? Only the very lucky intervention of Ragna, Jin, and Ky Kiske stopped Mu-12 from murdering more people.
To clarify, characters technically can go back in time in their worlds and change events as they're supposed to unfold. Doing so, however, results in both a heavy fine and being forced to go back and Set Right What Once Went Wrong. Characters who use in-universe technology to travel through time, however, like Lucca and Frog, are left be.