Anyone who may not have made the connection, the "I'm not Jigglypuff!" may have been a Shout Out to the memetic nightmare scene from Rugrats. "I'm not Tommy!"
When Dark Matter attacks Cocoon Academy, Ganondorf yells out, "what in Din's name?" At first, it seems like a reference to Din, one of the goddesses from The Legend of Zelda... but when you think about it, Din is the Goddess of Power, and Ganondorf wields the Triforce of Power...
In this script, Waluigi, and not Tiny Toad pops out of the bag in the last panel. Earlier in the comic, this script to be specific, we see Ashley's husband getting kidnapped. Have we made the connection yet?
Or Waluigi may have bugged Bowser with one WAA too many sometime before. Of course, Rule of Funny makes the previous theory more likely.
In a Mushroom Kingdom Christmas CarolPart 3, Wario leaves Wario Ware to go into the banking business with Mario because "video games are a dying industry, anyway." Later on, you remember that this is shortly after Bowser supposedly quit and the Mario Bros. celebrated their final victory. Video games were a dying industry because the guy who more-or-less put the industry on the map has just retired!
A Mushroom Kingdom Christmas Carol contains a subtle Throw the Dog a Bone that viewers may not have noticed the first time: In the time between now and when the story starts, Mario and Peach got more and more into their work and slowly drifted apart, while Luigi and Daisy married and adopted a child.
ThisBrawl in the Family comic is funny on its own, but we may not realize something brilliant about the punch line: Bullet Bill cannons never fire when someone is right next to them.
In the comic musical "Ode To Minions", there is a panel which has the singer say, "put your plumber's hat over your heart and say..." with an accompanying picture of Mario, Luigi, Wario, and Waluigi all doing so. Though Waluigi had his fingers crossed behind his back. This seems like Waluigi's usual deal when you realize, Waluigi has never fought any minions! If he's never had to do so, why would he feel sorry about it?
While this is true, Waluigi is likely crossing his fingers because he doesn't feel bad about any of the minions, not because he had no involvement with them. YMMV though.
Notice the lack of Sonic the Hedgehog in "Ode to Minions". I was confused at first, but then I remembered that all the mooks in the Sonic games are actually animals trapped in robots that Sonic is liberating.
In comic 386, Daisy was talking to Vivian about racing. ("It was just like that Wiggler just let me on through"). In comic 383, she found out that Wiggler racer had some Nepotism with the Wiggler on the track, Maple Treeway. Alt Text? "Now then, if you want me to be quiet, don't block me on the track either." See the connection?
Why is it Dedede is shown acting like a Jerkass to Kirby half the time, but a friend the other half? Well, notice how when Dedede and Kirby are being friendly with each other, they're usually indoors or somewhere where there aren't many others. It could be Dedede and Kirby are normally friends, but when in public, Dedede acts like a villain to keep up his image.
Given the revelation that the "Cocoon Academy" arc is from Meta Knight aka "Pinky"'s perspective, this comic makes more sense as an "Intermission" — Pinky's not in it at all!
In "Phillip's Box", we see Waluigi save the day by making the "evil" Philips CD-i spirits leave. We never learn what he did, but if you look at the last panel, you can see that his hands are on his (Hawaiian) shirt. ...which either means he's tugging it in accomplishment... or he's putting it back on...
Want this to be worse? In the same panel, you can clearly see that the suspenders for his pants aren't on his shoulders. Meaning....
A naked maniac follows you, maybe fireball-launching. Can you blame those spirits?
Considering it was only a few seconds, it's possible that Waluigi merely took his shirt off, possibly his pants too. Considering Ariel's reaction to Waluigi in a speedo in an earlier comic, it isn't too much of a stretch to assume that would be enough to scare off the spirits.
Also, if you follow the Waluigi thing above in the brilliance, think about it. An evil person married to the strongest witch. The possibilities are endless...
As Matt said in the mouseover text, "Resourcefulness" and "If It Takes A Lifetime". Mario re-lives his life 254 times just to get over a single pit!
In Ode to Minions again, you can see a Lakitu with a picture of his wife, who is in fact Flurrie, and his daughter. Then, Mario kills him. So Mario kills his friend's husband. Sleep well.