Mike using the Saved by the Bell Zack Morris Time Out is a callback to an episode of Cracked After Hours that aired the day before the Agents of Cracked episode.
Michael receives a phone call and guesses that the person on the other end is "Clippy". Clippy is the sidekick (consisting of video clips that follow a theme) of Michael's android persona in "Cracked TV" and "Does Not Compute".
Anything That Moves: Swaim takes Dan to a bar. Dan strikes out with the ladies, while Swaim goes home with every customer in the bar. And one dog. And a particularly sexy bar stool. Among Swaim's "quasi-legal fetishes" are Hot Wheels, making fart noises, and holding up either very small or very large charts. Regular-sized ones don't do it for him, though.
Arson, Murder, and Jaywalking: Apparently, Michael mails heroin to kids, makes bald eagle egg omelettes that he doesn't even finish, and rents video games, then keeps the manuals.
Michael Swaim used to be a judge. This comes up again during the goat sex case.
Ricky was blinded by one of Michael's 'pranks', in the Christmas Special, blinded Ricky is seen trying to feel his way out of the Cracked offices, along with DOB and Michael.
B-Tone is also reprogrammed by Sarge (after being blinded in both eyes) to fill in for "some employee who hasn't been showing up. Robby ... Rachel ... Ri-Ri ... Ricky ... some worthless piece of shit."
Mike meets DOB when he throws a bottle of booze off the roof of Cracked's offices. In the last episode of season 1, this is how DOB finds the presumed dead Mike.
Also, BEST FRIENDS THREESOME! (The Tragedy of the Fightin' Hogs in Season 1, and F.U.B.A.R.-king Up the Wrong Tree in Season 3)
In an earlier episode Chief tells Mike a story about how he cut off his third testicle with a corkscrew In the final episode, it's revealed that because of this, Mike, his only child, came out mentally challenged.
Another one that's easily missed; in one of the season one episodes during Dan's performance review with the Chief, he is forced to enter the Cave of Trials and fight himself in a Darth Vader costume. In the final episode of the series, it's revealed that the Chief is capable of cloning people. Evidently he cloned Dan twice.
All the way back in the third episode, Michael has a drawing of a dog labelled "BONERZ" at his desk, who he insists on introducing to Dan in the season 2 finale.
Among the various misconceptions about the East Coast that Michael states when about to meet/first meeting Dan, one is people on the East Coast traveling by hot air balloon. When Kelly comes to visit, she adds at the end of one sentence that she'll be taking the next zeppelin back east.
No one remembers Stuart's name. Not even Stuart's mother.
In a first season episode, Michael mentions his belief that everyone on the east coast goes to work in hot air balloons and sleeps in grain silos; in the series finale Dan and Michael go to the east coast by way of a hot air balloon, and DOB mentions (possibly jokingly) that Michael's going to have to sleep in a grain silo because "That's where we all sleep, back east." And a few episodes earlier, Kelly mentions having traveled to California via zeppelin, confirming another of Michael's crazy cultural perceptions.
Crazy Cultural Comparison: Michael believes that the "East Coast" is a foreign country where, among other things, everyone rides hot air balloons to work and sleeps in grain silos, "fag" is just a fancy word for "elevator", and the best thing Dan could hope for is to marry a soapmaker and sell scrimshaw scenes of The American Civil War to passing cattlemen until the day he dies of "heartstop".
Crazy-Prepared: Swaim has thousands of knives hidden all around the world, including on the persons of Secret Service agents, in case he ever needs one.
The Danza: Both Swaim and DOB are named after, well, Michael Swaim and Dan O'Brien.
Depraved Bisexual: Swaim. He seems veryattached to DOB, but he also has multiple wives, and he claims to have had sex with Mandy at least twice. In season 3, he orders a group of drunken bar patrons to line up in accordance with their positions on the Kinsey scale, and tells them that he intends to have sex with all of them.
Not just "all of them", "every part of them, in alphabetical order".
Don't forget the barstool. They're going back to his place. Perhaps making Swaim a Depraved Pansexual?
When Dan finds himself in the bar in season 3, he asks the bartender to serve him the most noxious, poisonous, self-destructive drink she can think of. He gets apricot brandy and Clamato.
Drugs Are Bad: Inverted. Swaim has a heroin addition and gets Dan to try it in "The Least Effective Drug Intervention Ever" ("A hit a day keeps the tremors at bay!"), and Swaim implies he's done crack in "Adpocalypse Now":
Swaim: Dude, I'm tellin ya, stuff is way funnier.
Early-Bird Cameo: Cody Johnston appears in the background of some shots, but just seemed to be an Easter Egg. In the final episode, we find out he's the Chief, who's been watching over Mike the entire time.
When DOB and Michael sneak into Broked Offices and crash the surprise party, B-Tone immediately leaves.
Escalating War: In one episode, Swaim thinks that he and DOB are in one—and that Dan started it—but Dan's "pranks" are entirely in Swaim's imagination.
DOB: Michael, I have never played a joke on you, alright? I need you to believe that we are not in some kind of trick murder contest.
Swaim:Prank murder contest.
DOB: I really wish murder was the word we were arguing over in this sentence.
Exactly What It Says on the Tin: Michael is told to make a "Facebook" for Cracked and assumes he's literally supposed to make a book out of people's faces. Terror ensues.
"It got easier when I remembered the children's cemetary.
Exotic Equipment: Michael has a "weird-looking dick" as the result of being the son of a demigod with corkscrew-shaped testicles. His member is apparently prehensile and can be used to type and hold up large signs.
Eyepatch of Power: The Sarge, whose patch has been noted to move from one side of his face to the other between cuts. The patch even briefly migrates onto Michael's face when he pretends to be Sarge, forcing Sarge to cover his eye with his hand. In the episode with the failed heist, Sarge is seen wearing two eyepatches, one of which covers a regular eye. B-Tone ends up with two as well.
It's mentioned Sarge wears it because of "redundancy".
Flanderization: Compare Michael in the first season to Michael in season three. Mandy gets it even worse.
Arguably, any character in the show. Dan, for example, goes from an average if somewhat Adorkable guy with some capability of standing up for himself to a complete and utter, terrified doormat. It even turns out he's a virgin after all. Sarge's flashbacks also become the rule rather than the exception.
Sarge arguably got it the worst, the fastest. I've never seen a character go from relatively normal, with bouts of wackiness, to screaming lunatic wacky all the time, in such a short amount of time.
It could, arguably, be justified- working at Cracked is terribly stressful, so maybe it just wore Dan down and made Sarge slightly crazy. As for Mandy... well, maybe she just is that shallow and we got to see that side of her only when she became one of the main characters. After all, the few moments she somewhat cared about Dan was when he did something like Mike (the first instance being when he made 'coffee').
It should also be noted that Mandy was also disgusted by Michael in Season 1. The only real explanation for why those characters went from being silly, but realistic (except Mike obviously) to caricatures is Rule of Funny.
Foreshadowing: In the second episode, Dan insists to Michael that they're partners as in "co-workers", not as in "gay guys".
Freaky Friday Flip: Swaim takes "bear Ritalin" and becomes more like DOB. In order to save his job, DOB becomes like Swaim. He becomes instantly more likeable to the entire office, forcing Swaim to admit he was faking it the whole time. Also, he's immune to pills. All pills.
Gainax Ending: Boy howdy. B-Tone, T-Bone's brother, comes to Cracked to kill Swaim, who it turns out is the Chief's son, and, since the Chief, who is revealed to be played by Cody Johnston, is a god, Swaim is a demigod. Swaim is his only son due to penile problems, and due to those same problems he came out mentally retarded, thus, Cracked was created to hide his existence, Broked as a fake enemy for the site, and T-Bone as a robotic infiltrator who was supposed to watch him but instead went all turncoat on Cracked. After this revelation, B-Tone, who is also a robot, has a huge offscreen fight with DOB, Swaim, the Chief, and Sarge, leading to DOB and Swaim having to drop off the map for a while because it will be made publicly known that they are dead. They then fly back to the East Coast in a hot air balloon and start making out. Roll the credits!
Idiot Savant: The Chief actually calls Swaim this, and it's shown that he is actually an excellent writer.
And an excellent judge.
Impossible Thief: A girl Dan had a crush on becomes one. Stealing the clothes off their backs and swapping them around. And then when leaving steals a bunch of office supplies and the ice cream off a ice cream cone Swaim was eating.
Indy Ploy: Apparently a lot of articles from Michael are made on the spot.
Initiation Ceremony: Apparently one of the requirements put on Dan to join the Cracked staff was to kill a man.
The Internet Is for Porn: Swaim's immediate conclusion upon discovering Google. "I typed in 'porn' - and porn came up! I typed in 'breakfast' - and porn came up!"
Kavorka Man: Though not physically unattractive (with the arguable exception of his clothes), Michael's personality would seem to make him an unlikely lady's man. But almost all the women on the show, and quite a few of the men, are attracted to him. Including Dan.
Konami Code: "A man has to have a code, Daniel! And mine goes up, up, down, down, left, right, A...I'm sorry: up, up, down...F*** me, I think I recorded it..."
Lampshade Hanging: Throughout the body-switching episode, constant reference is made to, well, body-switching.
Dan: Really? I mean, I can't believe we're stooping to that... as a website.
Laughably Evil: Swaim. He drops empty liquor bottles on pedestrians from the roof of Cracked's offices, keeps his multiple schizophrenic "wives" imprisoned in his house and car for six years, has crippling addictions to heroin and jetski polish, wears skin suits, and is the Zodiac killer, but he's a deranged, comedic savant and all of it is played for laughs.
Metaphorgotten: "I'll tell her the deal's off. ...Then I'll tell her my pants are off! Then I'll tell her there's a new deal! And then I'll tell her 'Frankly, I'm about to Delano all over your Roosevelts.'"
Dan: That kinda got away from you, huh?
Michael: I don't think it did.
Mistaken For Pedophile: When Mandy calls Dan's choice of drink "juvenile yet mature", he quips "I love combining my man-parts with those of a child."
The Mole: T-Bone, subverted when it's revealed in the finale that he's actually a glitching robot.
Or So I Heard: A running gag from Swaim about the Chief in Season 1.
Given a nod in the first episode of the second season. The Sarge is convinced that if he refuses to take the position The Chief will shrink down, climb into his brain and force him to do it. And when that's debunked, he thinks he'll go back in time.
Daniel: You must understand, our entire editorial process is basically a toxic containment system meant to prevent Michael's real personality from ever leaking out into the world...
Canonized when it is revealed that the entire Cracked website was created to keep Swaim occupied and distracted.
Rashomon-Style: The plot of the fourth episode of the third season, told to The Chief from the perspectives of Mandy (who is physically incapable of noticing Dan's presence), DOB (Who, despite arguably having the most accurate flashback, tends to see the world as a depressing black void), Swaim (who sees the world as a psychedelic nightmare), and Sarge (who is constantly living out a Vietnam flashback).
Retired Badass: The Chief's current replacement since he decided to take some time off in Season 2. The Chief had to find him by hiring the world's best assassin and then following that assassin.
Running Gag: Very subtle, but Sarge's eye patch is constantly switching eyes. In a later season 3 episode, it switched entire bodies.
Rummage Sale Reject: Swaim dresses like this in every episode. DOB runs off to "the thrift store and the gay neighborhood" during the body-switching episode to procure a similar outfit.
Self-Deprecation: "So what're you gonna do with the company now that it serves no purpose beyond compiling lists of infantile dick jokes?"
Swaim and Dan are caught sneaking into Broked.com's office, and are interrogated by an identical team played by themselves. Much to Dan's dismay, this leads to Screw Yourself.
Same episode, a blink and you miss it appearance of T-Bone's robot double, B-Tone.
It turns out that Broked.com is staffed by clones of everyone at Cracked.
Sound Effect Bleep: Done intermittently. The final episode features a montage of all instances of this. Probably due to Rule of Funny, sometimes "shit" and "fuck" will be bleeped out, and other times not.
Start My Own: The second to last episode of the first series has a case of this. After Swaim gets fired for supposedly leaking Cracked secrets to their rival Broked, Dan asks him what he's going to do. Swaim intends to make his own version of Cracked, completely by himself. Considering that he's an idiotic, comedic savant who is literally homeless from this incident, Dan has his doubts.
Swaim: I'm going full ronin on this one. I'll wander from town to town starting my own multinational humour outlets.
DOB: ... That is a big process, and I don't think you're qualified for any... ANY one aspect of it. I don't believe there is a single step you could handle. I mean, do you even have a place to stay?
Your Head Asplode: The function of Dan's 'Failsafe Device'. Apparantly it's not lethal. This may be due to Michael's apparent immortality, as he later claims that if Dan kills him, he'll come back 'so hard'. Later, this is revealed to be because he's a demigod
WHAM Episode: Ohai finale! Where should we begin? Well the Chief turns out to be Cody, who is also Michael's father. Because the Chief is part of a ancient order of demigods, and Michael is too "retarded as balls" to be his offspring, the order would want Michael killed if they found out. After all, "you can't have a retarded demigod running around." So the Chief created Cracked as a way to keep Michael occupied and hide him from the other chiefs. In other news, Cracked's rival Broked is staffed by clones of the Cracked staff (oh yeah, the Chief also created cloning), the articles and videos on Cracked.com are encoded with the ultimate truths about the nature of life, the universe and everything, which can be decoded (or, if you will, "cracked") by anyone who reads every single article and buys the right merchandise and T-Bone (and B-Tone) are robots reprogrammed by the other chiefs to kill Dan and Michael. So of course, Dan and Michael fake their own deaths, and they all live happily ever after. Am I missing something? Oh, yeah, Dan turns out to have been in love with Michael all along. All this in 12 minutes and 40 seconds. Whew.
Sarge: "So, what are you gonna do with the site now that it has no other purpose than as a repository for dick jokes?"
Chief: "I don't know. Sell some hats?"
Yandere: Swaim is alarmingly attached to DOB, and genuinely seems to consider him his best friend. However, this won't stop him from unthinkingly ruining anything positive in DOB's life if it will bring Swaim personal pleasure.
Swaim: One day we will be best friends, or die trying.