- In "Two Mites Make It Wrong", Daphne and Batman manage to (metaphorically) talk the monster to death when the Scooby gang and the Dynamic Duo get caught up in the middle of a fanboy spat between Bat-Mite and Scooby-Mite.Daphne: Hold it! In the first place, it doesn't matter whose hero is the best. We all contribute what we can. That's why we all work together! Besides, you say you're Scooby and Batman's biggest fans? If that's true, why would you want to change them? You already think they're great the way they are!Batman: Daphne's got a point, fellows...If you already love watching our adventures, then why not just go home and let us have more of them?Bat-Mite: Uh, well...Scooby-Mite: When you put it like that...
- In "A Superfriend in Need", Velma uses Bizarro's backward logic to get him to leave Shaggy and Scooby alone and attack Grundy, Grodd, and Cheetah instead. After all, Shaggy, Scooby, and Velma are his enemies; the Legion members are his friends.Velma: So what does that mean?Bizarro: Bizarro fight friends!
- When Sinestro shows up, he manages to defeat and shrink the Justice League, only to be confronted by Shaggy and Scooby. He raises his ring to attack them only for Shaggy to completely unintentionally alter his Yellow Lantern ring's output. Said ring then declares Shaggy a true Yellow Lantern due to causing himself so much fear and flies to rest on his finger; Shaggy then effortlessly reverses all of Sinestro's misdeeds
- In "Trouble in Paradise", Nubia, one of the Amazons, insults the entire male gender based on Shaggy's cowardice. Wonder Woman is quick to correct her. It's nice to see one of comics' most iconic superheroines actually promoting the idea that "All people have the potential to achieve great things", rather than "Women are better than men."
- In a meta-sense, the comic had the balls to actually feature Danny the Street of all characters without worrying about whether or not he'd be inappropriate for kids (you know, being a gay transvestite and all).
- In the Legion of Super-Heroes crossover, Mystery Inc. actually beats more of the Fatal Five than the Legion themselves! Daphne beats the Persuader with a martial arts move that sends him flying over her head, Freddie takes down Mano by pulling off his mask and exposing him to an atmosphere he can't breathe, and Shaggy subdues Validus by offering him snacks and letting him pet Scooby.
- In 'Perils Before Swine', Mystery Incorporated is able to do what Penelope and the Ant Hill Mob have been unable to do for so very long: unmask The Hooded Claw and finally expose Sylvester Sneakly for the crook he is, leading to Sylvester being sent to jail. Penelope wonders what she'll do with her new found free time.Velma: We were wrong to judge by appearances. After solving so many cases, we should've known that the monster's never the person who looks guilty!
Fred: (grabs Hooded Claw's costume) Right! It's always the person...
(Fred pulls off the costume of the Hooded Claw to reveal... Sylvester Sneekly!)
Fred: ...you'd least expect!
Penelope: Sylvester Sneekly?! You've been the Hooded Claw all along?
Sylvester: Aaaah, I could deny it, but why bother? I'm glad I don't have to keep up this charade anymore! You think it's easy to dream up all those perils? Who needs the aggravation?
Daphne: We'll call the real police to deal with the Hooded Claw and the bully brothers. No more perils for you, Penelope!
Penelope: Gracious! Whatever should I do with my time?
Dum Dum: Gee, Penelope... With no more perils, I guess you won't, uh, need protectors anymore, huh?
Penelope: Why, I suppose that's true, Dum Dum. I won't need protectors... But I'll always need my friends!
(As Penelope and the other celebrate, Sylvester and the Bully Brothers are arrested by the police.)
- After all the time Fred spent in A Pup Named Scooby-Doo accusing Red Herring of being the culprit, come "A Crisis of Infinite Scoobys" he can finally say Red was the culprit and this time he got it right!
Awesome / Scooby-Doo! Team-Up