The animation of the building being demolished during the movie Arthur and Buster watch is from D.W.'s Baby. It was also previously reused on Meek For a Week.
When D.W. put on the incandescent light bulb, from the play that Mr. Ratburn's class did in Francine Frensky, Superstar, Arthur calls it his costume. But Arthur wasn't the incandescent light bulb, he was the phonograph. Buster was the incandescent light bulb.
Although most of the flashbacks in D.W.'s Perfect Wish are clips taken from older episodes (with the music replaced), the flashback to when Mr. Rogers is at their house actually features new animation of Mr. Rogers singing to D.W. as she is sleeping in bed (in the original episode, Arthur Meets Mister Rogers, he was singing the same song to Buster and D.W., whom was awake at the time).
In this show, DW turns 5. Presumably. But nothing changes. The following episode, she's still 4.
In "D.W.'s Perfect Wish", Arthur reminds D.W. of the time she got the chicken pox from him, and she says "That wasn't fun." Actually, D.W. was overjoyed when she came down with them because of all the special treatment. (Watch "Arthur's Chicken Pox")
Muffy mentions in this episode that she remembered George from back in kindergarten, but in another episode she said she was a new student that first appeared in the class in second grade.
In the story Night Fright, Arthur says he's afraid of ventriloquist dummies. However, his fear seems to have vanished in George's Dummy Disaster.
In "What Scared Sue Ellen," Buster doesn't wear a shirt under his jacket.
While the Library Card and Jekyll and Hyde songs consist entirely of new animation, the other two songs Leftovers Goulash and Homework contain no new animation, and instead are compiled of stock footage from previous episodes.
In "D.W. Tricks The Tooth Fairy," D.W. remembers that when Arthur tried to lose a tooth, he chewed gum. We are then shown a clip of him chewing taken from "Arthur's Tooth." But in the episode, what he was chewing wasn't gum, it was rock candy.
When D.W. gets hit with the swing, a swing on the swing set disappears.
The clip of the world blowing up during the Turbo T-Bot show's opening sequence comes directly from "Arthur Goes Crosswire;" the scene where the gang plays a video game where you destroy planets. You can even see the video game score, etc. during that shot in the opening!
CTKDX69- D.W. looks like she can read what the calculator says, but she can't read. -CTKDX69
CTKDX69- When they show the clip about D.W. showing the necklace to Arthur, he is thinking, but in the original scene he has a sly face. -CTKDX69
During the maze scene when Arthur thinks his shadow is moving, he falls backwards, but in the next shot, he falls through a maze wall tearing it up.
The sorcerer has a different voice when Arthur gives him the sword.
Binky's song is called "Matalii ja Mustii" and is sung by Värttinä.
One of the rocker kids who are doing all the grafitti is a caricature of a character designer from his rocker days in the 1980's. Unfortunately, the voice director cast a girl voice for him.
Look closely: in And Now Let's Talk To Some Kids, the map on the geography quiz Mr. Ratburn gives the kids has the Soviet Union on it! (It's in Asia, where Russia is now.) The Soviet Union broke up in 1991, five years before the show started airing.
In "Arthur Goes Crosswire," kids are already outside before the school bell rings. Most noticeably Muffy, who sitting in her limo.
She was also on the phone with her father, meaning that she must have been out there a while if she had time to call her father and tell him about Mr. Ratburn's project.