The Season 1 episode "Meek for a Week" has Muffy and Francine bet on a Princess Peach watchnote This may be entirely coincidental as 1996 was the year that Princess Peach became known as "Princess Peach" in the West rather then "Princess Toadstool" and video game references are non-existent in Arthur.
Episode 9 of season 3 is titled "The Return of the King", a reference to the title of the final book of The Lord of the Rings trilogy.
S14's "Falafelosophy" has guest-star Neil Gaiman appearing in Sue Ellen's falafel as her personal muse. Not unlike what the The Lord of Dreams might get up to.
A number of other celebrities appear as guest voice-actors on the show, and many times, they are, in fact, playing themselves. These include Jack Prelutsky, Art Garfunkel, Yo-yo Ma, Philip Seymour Hoffman, Koko Taylor and others. The complete list is here.
S13's "The Secret Origin of Supernova" was basically one big Shout-Out to comicdom, including a reference to Jack Kirby.
The Cold Open of S8's "Bleep" features a clip from an episode of The Altos. Apparently, Marc Brown is a fan of the show.
S6's "Sue Ellen Gets Her Goose Cooked" contains a reference to Citizen Kane with Muffy's old game room containing a sled with the word "Rosebud" written on it.
In S6's "Arthur and Los Vecinos", Arthur objects to wearing a bowtie, saying the only people who wear bowties are nerds, waiters and "that science guy on TV."
In S7's "Pick a Car, Any Car", the names of Mr. Crosswire's salesmen are Romero, Gorshin, and Meredith, named for the actors who played the Joker, the Riddler, and the Penguin respectively in the 1960s Batman series.
In S8's "Desk Wars", Muffy had stickers of the "Judo Kittens", which look a lot like kitten versions of The Powerpuff Girls.
In "That's a Baby Show!", Buster mentions a Dark Bunny villain named Doctopus, which totally flips the concept to an octopus going to medical school and becoming a doctor.
S4's "The Contest" is full of these:
In addition to being a parody of Arthur itself, the characters in Show Within a ShowAndy and Company are dressed and drawn in the same way that characters from The Little Lulu Show, with the D.W. look-a-like dressed as Lulu herself and The Brain look-a-like dressed as Tubby.
Buster's story has the art style of South Park, and even references a certain running gag:
Francine and Binky's story involves Arthur in WWE taking down Hulk Hogan, and then it's announced that he will be facing off against John L. Sullivan, Floyd Patterson, Barney Rose... and the United Press International.
Arthur's story has him visiting his therapist, Dr. Katz.
When Pal is attacked by Killer, Pal immediately yells that "It's A Trap!"
This certainly wasn't the only Star Wars reference. In "Arthur Loses His Marbles," Arthur has a fantasy-sequence in which a Yoda-like Grandma Thora tells him "Talent you have. But no patience. Or humility. Much you have to learn." In "Arthur's Faraway Friend," an imagined Buster tells Arthur to "Use the Force," but when asked what this means, admits he "just thought it was funny."
In the same episode, the same scene actually, the prisoner that Binky breaks out of jail with is William Carlos Williams, a poet known for his free-verse poems. He is shown shouting "Free-verse! Free-verse!" through the bars of the jail cell in protest.
The title of "I Wanna Hold Your Hand" is likely a reference to the song by The Beatles.
"D.W. Talespins" has D.W. trying to come up with a better story than the 'Vegemorphs' series, an expy of Animorphs. The cover is even in the same morph-stages style as the real books (interestingly, there actually is an Animorphs parody called Vegemorphs, but it isn't like the one shown here).
In episode 3x10, Attack of the Turbo Tibbles, the Tibble twins are flipping channels and come across a show with two characters that have designs similar to The Busy World of Richard Scarry and note "Too busy, not scary". (Might count as Self-Deprecation, as Cinar produced both shows.) Also the show the Tibbles become obsessed with, "The Terrific Trooper Toy T-Bot Team" is a parody of Mighty Morphin Power Rangers
The circus camp from S9's "Francine's Big Top Trouble" is Circus Smirkus in all but name.
In S14's "The Long Road Home", there are occasional shots of a map showing Crown City and Elwood City as George, his father, and Mr. Ratburn walk from the former to the latter. The map is the greater Montreal area with the place names removed.note If the place names were filled in, Crown City would be just outside the suburb of Brossard, while Elwood City would be near the suburb of Saint-Eustache. This was a reference to the fact that a large part of the series' production at that point took place in Montreal, which is/was home to many of the voice actors.
In "Buster and the Daredevils", a shoutout to Beavis And Butthead appears in the form of "Peabrain and Nuthead".
In "The Friend Who Wasn't There", Muffy imagines the characters from The Wonderful Wizard of Oz, played by D.W., Arthur, Buster and Francine, trying to follow the Yellow Brick Road in her family's mansion's basement.
"Shelter from the Storm" features Idina Menzel as a counselor Brain sees for help getting through the trauma of a hurricane damaging his family's ice cream shop. Her character references singing, and at the end of the episode, she shows up at the ice cream shop, saying she loves all things sweet and...frozen.
S8's "Fernfern and the Secret of Moose Mountain" has a lot of references to Tintin in the form of Zutzut, a comic series Fern likes.
Season 13 has some rather adult references. "The Pride of Lakewood" begins as a school pride story and quickly turns into a toned down version of The Wave, while "Looking for Bonnie" features an imagine spot in which Buster befriends an alien in a guitar battle not unlike the iconic scene from Deliverance.
Season nineteen's "Maria Speaks" is almost certainly named for Arthur's fellow PBS show, Martha Speaks.
Season 19's "Carried Away" features Pal's alien cousin Dr. Yowl from Pluto, a reference to Doctor Who, with the BARCDIS based on the Doctor's TARDIS.
Likewise, Season 21's "The Princess Problem" riffs on the naming convention used for most episodes of Peg + Cat.
There's an episode where Arthur stares, distraught, at his hand, which is covered in sticky fluid.
"Jenna's Bedtime Blues" has the titular character watching a hybrid of Sesame Street and Wimzie's House where puppet characters teach the letter P to viewers. (The latter show was also produced by Cinar.)