All Just a Dream: In "A Trip to Teletubbie Land", Mario has a nasty accident while fixing the castle pipes and ends up in a land full of Teletubbies. At the end, it was revealed to be dream, but the pipes weren't fixed yet.
Every Mook in Operation G.A.Y was a sprite of Luigi, some of them wearing a Princess Peach dress.
Art Shift: Done deliberately whenever a character is doing something not possible in Super Mario 64, where Garry's Mod models are used instead.
Possibly the biggest examples are in "Retard Karts 101", where because of the lack of Garry's Mod models done in SM64 style, Luigi shifts from being a recolor of Mario to a black-eyed plush which resembles Luigi's colors in the Mario canon more closely. This is only excluded during closeups of Luigi's front side, where he returns to SM64 Luigi.
Peach, Wario, and Waluigi after he goes buff swap to their modern counterparts when driving their karts, while Wario returns to a Mario Party model in front-angle closeups.
Asian Speekee Engrish: the Japanese islander later revealed to be SMG3's henchman when SMG4 meets him a second time in "Super Happy Magical Fun Fun Island".
Big Damn Heroes: The policeman in "Birthday Freakout", followed in the next episode (Luigi's Retarded Mansion) with Dr. Robotnik saving Luigi from a possessed chair.
In "Mushroom Wars", to save R2-D2 from a flock of Teletubbies, Mario winds up almost attacked by them until SMG4note named "Hobo-Wan-Konobo" in this special barges into action and saves Mario.
Big Eater: Mario has been shown to scarf down 35 bowls of spaghetti in exactly five seconds.
Big "NO!": SMG4 when he's about to be squished by Gourmet Guy in "Mini Italians".
Blatant Lies: Mario claims to have never used Scatman John's music in his life.
Body Horror: While certainly not Squick levels and just Played for Laughs, Toad's "dance" has his head detaching and rotating 90 degrees clockwise reattaching on it's side, and his limbs merging into his body.
Brown Note: Mario is forcefully clad in rainbow clothes in "Scatman's Revenge" that cause weird things to happen to anyone who sees him.
Butt Monkey: Of all the characters in the series, Toad gets hit the worst, especially in episodes that only feature Luigi the residential Chew Toy as an one-off background character.
Flashback Cut: Done with the numerous times Mario invokes Scatman John's music in "scatman's Revenge".
The Fourth Wall Will Not Protect You: After examining his cursedclothes' effects on the characters, Mario asks the viewers if they still love him... and then the video drops in quality and gets static playing over it. Oddly, Mario is aware of this.
This isn't the first time this happened in the series though. "Switcheroooveralls" had a similar plot.
Done again with Mario and Steve in "Mineswap", where Mario becomes a Minecraft character and Steve (aside form getting lighter skin) a Super Mario 64 character. Steve seems quite happy with the swap, while Mario gets very frustrated (such as not being able to turn the knobs on doors with his blocky hands and destroying toilets). They fail to get it reversed in the end.
Great Escape: "Crime Time" and "Party Rock Prisoners" has the characters(s) trying to break out of jail. The former blooper has Mario helping Luigi escape from jail. The latter blooper has Mario and Toad trying to escape from jail together.
Greedy: Mario when he won a million coins in "Rich Glitch".
Groin Attack: In "Mushroom Wars", Peach performs one onto the Trooper that is trying to flirt with her.
Mario almost got this at one point in part 1 of "A SM64 Fairytale" after accidentally killing the princess with a fridge. He does get beheaded in the finale of the Fairytale episodes trying to defeat a giant Bowser.
SMG4 loses his head to a intoxicated Mario in "Free Lunch for Mario".
For a short time in "Mushroom Wars"' first part, L-3Ginote Luigi as C-3PO loses his head in the jet crash next to Mario's farm. He retrieves it eventually.
Oh Crap: Frequently; for one example, Mario freaks out when he sees the giant clone of himself running towards the castle in "Scatman's Revenge".
Palette Swap: Almost every Original Character is a recolor of Mario. Even his own brother Luigi suffers the same fate, despite there existing customized and playable Luigi models in select Super Mario 64ROM hacks.
Eventually this would be lampshaded in "The Mario Parable" with the narrator pointing out how everyone looks exactly like Mario.
There are also a couple of Peach recolors present, mostly to colorize her like Daisy. However they are not as common, nor were they brought up in the above-mentinoed lampshading.
Averted with Wario and Waluigi; previously they played this trope straight, but starting from "The Wacky Wario Bros", they use green-screened models from the Mario Party series.
Paper-Thin Disguise: Mario and Bowser wear Toad hats in "A Fungus Among us" to get into Peach's castle after it's raided by Toads. At first it works, even after the cap falls off Mario in his initial visit of the invaded castle. Only after it falls of a second time does the disguise fail.
President Evil: Toad when he becomes president for a day in "President Toad Washington"
Trademark Favorite Food: Mario loves spaghetti (or as the series spells it, "sphagetti"). His extreme love for it is often shown in situations where Mario does not want to be part of... and then whoever wants him to come with them (SMG4 in most cases) tells them that spaghetti is in danger and Mario joins along.
Zombie Apocalypse: When Mario ended up travelling 10,000 years into the future in "Castle Jumping = Time Travelling = Zombies", his future self used his time machine to get the present Mario back to his own time, but an accident sets the setting on the machine to "random". They end up in the year 2075, the year of the zombie apocalypse. With the help of X, the zombies were countered.