Along with Wario's short lived band Tommy Fungus and the Dungeons.
April Fools' Day: Episode 55 was delayed for two weeks, replaced with a video PSA about smoking by Snake.
The same thing was repeated with Episode 68, only with a skit featuring Julian (Snake) and Austin (Brock) where Julian plays Resident Evil 4. Richard hilariously lampshaded the fact people fell for it the second time around.
Repeated in Episode 61 with Tommy Vercetti. Seriously.
Bond One-Liner: "Goodbye Mr. Vherestorm. It was nice meeting you" After Waluigi kills Blaire Vherestorm.
Booze-Based Buff: In the finale, when Captain Morgan drinks some rum to fight, it gives him effects like the Invincibility Star.
Boy Band: Johnny Mushroom and the Kingdoms - they even do music videos from time to time, and are often said to be better than the Jonas Brothers.
Bread, Eggs, Milk, Squick: Blaire's offer for Ken to join the Trifecta was a promise of $10,000 and Chun-Li's head on a stick.
Breaking the Fourth Wall: Happens quite often, the best known example being when Snake, Otacon, and Ash visited Richard to make him edit their entire trip to Merlin's Table. Later, when the Darkness approaches Luigi and Wario in an attempt to start an alliance, they say he will have to wait a week (the episodes are released once a week), after which the Darkness objects and says he is sick of breaking the fourth wall.
The example that will stay on all fan's minds is Mario's last words: "Thank you for giving me the best five years of my life."
Most episodes of any season before the season's respective Big Bad shows up about halfway or three fourths of the way through.
All but the final episode of Season 1.
Brick Joke: In "The Interactive Adventure," Luigi ended up inheriting amansion. In the first episode of Season 4 he sold it for a life supply of USB flash drives so he could never run out of memory. In Episode 53, Mario returns after he gains his memory back prompting Luigi to suggest a flash drive.
At the beginning of Season 4, Snake claims that he saw his brother Liquid (whom he believed to have killed in The Movie) drinking Starbucks. When it is revealed Liquid is alive we find out Blaire recruited him to the Trifecta by finding him drinking Starbucks.
Cerebus Syndrome: The very first season was largely centered on the Mario Bros. goofing off until Episode 15, after which they became much more serious while alternating between their serious and goofy selves: in Season Four, every character is a clever mix of both their serious and goofy selves, or as Mario puts it in Episode 57, "seriously funny."
Chuck Cunningham Syndrome: Ash, Peach, Daisy, Otacon and several others were forgotten after their appearances in the Move and Operation: Blind Storm. According to the Subscribe Voice, Ash is living back in Kanto and Episode 75 suggests Peach is back in the Mushroom Kingdom waiting for the Mario Brothers. The rest still don't have an explanation for their absences (Something which the Subscribe Voice lampshaded).
Christmas Special: In which UPS intern Francis makes a mistake, resulting in the Mario Brothers believing that the other brother did not get them a Christmas present.
Cross Over / Massive Multiplayer Crossover: Nox Decious is actually a character from RMA Studios' King Arthur series. Although, none of the films featuring him have been released. In season 3 we see Merlin, who was also in their King Arthur series; then in Act One of the Movie we see their other works, plus one video from a companion channel.
Grand Finale: Episode 75 (or its title The Super Mario Brothers) which is the longest episode of the whole show. Most episodes are close to ten minutes. This one is over an hour.
Halloween Special: Two in fact, one was a short spin off that didn't present much besides Halloween stories and only had Mario, Ash and Brock in it and the other was The Interactive Halloween (in which Freddy and Ghostface try to kill the Mario Brothers.)
Mario himself has even shown this throughout the show, but it shows up most prominently in Season 4.
Killed Off for Real: By the end of Season 5, the people well and truly killed off are Ganondorf, Nox Decious, Darkness, Blaire Vherestorm, Scott Masterson, Liquid Snake, Tommy Vercetti, Merlin and Link. (although Link will reincarnate sometime in the future)
And then the Master Sword in Season 5. Since it's the only thing that can defeat Ganon.
Man Behind the Man: Ganondorf is effectively behind most of the major conflict in the series; he was involved in the first revival of Nox Decious, who in turn created the Darkness, who in turn created the Trifecta, who paved the way for Ganondorf and his army.
Manipulative Bastard: In Season Four, Professor Oak willingly tricks Gary and Brock into doing several mundane tasks for him just so they could find out from him which one of them sucks more. Oak eventually claims they equally suck for not turning down the tasks. As a result the two fight over which one of them hates each other the most which Oak uses to his advantage once more.
Medium Awareness: Plenty. For example, Wario complains about being unable to get a flashback.
Merged Reality: Ganondorf's real plan is to combine the Real World and the Dark Realm.
New Job Episode: In Season One, where Mario and Luigi are tired of plumbing, decide to try out a bunch of jobs but fail every time.
No Name Given: The "Package Delivery Men" are only known by the company the represent.
No Pronunciation Guide: Ryu's name because of how Richard always pronounced it Rai-Yu instead of Rie-Yu when he was younger.
Justified as a lot of people unfamiliar with Japanese names probably did the same as him, too. Whatever the case, though, it's still interesting to note that he chose to mispronounce it due to thinking the actual pronunciation sounded too lame, according to a forum post he made.
Waluigi has this happen when Waluigi gives the others his powers and falls into a coma, thanks to the actor living quite far away. He then returns in Season 5 only for him to overstrain himself and become stuck in and out of consciousness.
Brock, played by Austin, has the same problem but managed to come back for Season 4 and 5.
Peach and Walgina had this happen for a different reason—they've since broken up with the main actors.
Link as claimed by Ganon in Season 5 got trapped in the dark realm by him.
Super Smash Bros in several instances like mention of Roy getting replaced by Ike.
Luigi's entire story in "The Interactive Adventure" is a Shout Out to Luigis Mansion.
In Season Three, Master Miller's appearance and Snake, Otacon and Ash's journey to destroy the Nether Saber is one to Metal Gear Solid. As Wario like Liquid was actually Master Miller and him tricking Snake into activating the Nether Saber is like Liquid tricking Snake into activating Metal Gear Rex.
Wario's temporary costume from Season 4 is his biker outfit from Wario Ware.
Though there's no official one, the Ash and Brock series comes close.
Richard has also said on multiple occasions that he plans for a UPS Spin Off (now confirmed as an Interactive Adventure).
Austin (Brock) and Daen (Professor Oak) produced their own spin-off name ''Stupid Pokemon Friends'' that follows on Brock and Oak's adventures after StMB ends. Sadly conflicts with Richard and RMA resulted in it being cancelled after one episode.
Spirit Advisor: Merlin acts as this during Season 5. The Darkness and Link join him in the finale.
Throwing Your Sword Always Works: during Wario's battle with the Darkness in The Movie, Wario pretends to be dead and hurls his Beam Saber through the Darkness' gut, which seemingly kills him. However, as Waluigi failed to bestow a counter-curse upon Wario before his prolonged absence, the Darknessis still immortal and gets back up later on.
Darkness: Gee, that stung!
Title Drop: Bowser in Act II: "THOSE, STUPID, MARIO BROTHERS!".
Toilet Humour: Quite a bit. While justified by the source material (as Wario has a fart attack), it is disliked by several fans. This caused a funny Take That by Julian (Snake) over the forums:
If you guys hate toilet humor, then you're going to hate the next episode when I eat poop and smear it on my face while throwing it at Mario's face and then swimming in a diarrhea fountain.
Link was originally played by someone else (the voice at the end of Season 1) but he was unavailable for Season 2.
Christian (Ryu) could've played Kid Icarus in Season 2
Julian (Snake) was a big fan of Resident Evil 4 and wanted to be Leon in the show.
Dane was given the option of playing Ness or Ash. He chose Ash cause he loved Pokémon. Too bad it didn't last.
Richard (Mario and co-creator) during Season 1 almost wrote several episodes that took place before Mario's very first trip to the Mushroom Kingdom, where he was a normal teenager working part time at a plumbing company, and where Merlin opens the portal to the Mushroom Kingdom and gives him his hat. However he and Chris (Luigi and co-creator) decided that is was too much backstory for a comedy show.
What was in the letter meant for Mario in Episiode 22?
The $8000 Mario and Luigi got from the Mafia. Word Of God claims they used it to pay Max Payne.
Temari, Ken's girlfriend whom he blamed Ryu for leaving him did not appear or get mentioned in Season 5 when the two make up. Richard stated that he decided not to include her but would later regret it since it creates an obvious plot hole.
"Where Are They Now?" Epilogue: Episode 75 has one clearing up the fate of all the characters. It's accompanied by a cover of the Carole King's So Far Away by UPS.
Brock and Gary are happily throwing and catching a Pokeball.
Ken and Ryu have recovered and are having fun.
Bowser returns home with Kamek.
Pauline and DK wed with Brock as the preacher, Yoshi and a pirate as best men and Mona as the bridesmaid (who catches the bouquet).
Ness is meditating and then gets up and walks off presumably at peace or having his own adventure.
Professor Oak is dancing at his house.
Yoshi is on his own eating an apple.
Snake and Naomi are still making out.
Zubashi and Gangles walk of Chili's with full stomachs.
Waluigi wakes up with Wario by his side. The two embrace and say goodbye as Waluigi leaves to live a normal life with Walgina.
Wario walks off happily with Mona.
The Mario Bros. end the montage with their businesses cleared and ready to go back to the Mushroom Kingdom. Before leaving Mario turns to the audience and says "Thank you for giving me the best five years of my life.".
Wimp Fight: Appears a lot in a form called "Slap Combat"
Woman Scorned: Pauline but she doesn't really target Mario or try to kill him. But she still blames him for it all.
Word of Saint Paul: Kevin Chamberlain (Yoshi) owns a youtube account here where he often does a series called History of Stupid Mario Brothers (inspired by Linkara'sHistory of Power Rangers) which shows his own opinion on the show and confirms several things in real life that Richie hasn't.
The creators and actors tend to go on the Fan Forums to answer fan's questions. A fan should be warned they don't go on as much as they used to, although Season 4 has already contained characters suggested by fans and fans had bombarded them with villains for Season 5. With Season 5 over they've been a bit more active reading fan's reactions and input.