Dakota mentions "a potted plant" as something that could potentially sabotage the pistachio protectors' mission, a reference to the time that Dr. Doofenshmirtz was foiled by a potted plant.
The pursuit of the t-shirts takes Milo, Zack, and Sara down some abandoned and derelict ski jumps clearly labelled as "Danville Ski Slopes".
At the end of a bet, Dakota has to dance with pistachios in his pants, causing squirrels to get in them. An instrumental of S.I.M.P. is played during this scene.
In "The Llama Incident", there's a blink-and-you'll-miss-it poster for Llamacoaster: The Musical.
In "Missing Milo":
The girl in the comic book shop is reading a Ducky Momo comic.
Dakota and Cavendish have a discussion about whether Cavendish is flooding (as in failing to start) a vehicle, which happens again in "Fungus Among Us". Phineas and Ferb have the same exchange in "Summer Belongs to You!"
In "World Without Milo", a truck driver sings the song "Meatloaf".
In "Love Toboggan", Milo sings a parody of "Boat of Romance", a song from Phineas and Ferb.
In "The Island of Lost Dakotas", Milo mentions that shoelace tips are called aglets, a fact that was the focus of the Phineas and Ferb episode "Tip of the Day".
In "Fungus Among Us", Dakota declares that "I'm handsome", a possible reference to a song sung by Dr. Doofenshmirtz (who shares the same voice actor).
"Milo's Halloween Scream-a-Torium!":
Zack asks, "Aren't we a little too old to be dressing up for Halloween?", a reference to the "Aren't you a little young?" Running Gag in Phineas and Ferb.
After plunging into a snowdrift, Savannah's hair falls over her face, making her resemble the "Grievance Girl", a horror movie character in Phineas and Ferb.
One of the trick-or-treating children wears a costume that looks like Perry the Platypus.
At one point, Cavendish and Dakota don costumes that resemble Phineas and Ferb.
In "A Christmas Peril", instrumentals of both "S'Winter" and "Candace Party" can be heard.
One pair of students participating in "Cake 'Splosion!" comes from Badgertown Middle School. Badgertown was referenced in "It's a Mud, Mud, Mud, Mud World", and even visited in "Der Kinderlumper".
In "Picture Day," the school marquee displays the text "THERE ARE ONLY 82 DAYS IN SUMMER VACATION AND THAT'S 104 DAYS AWAY." Of course, Phineas and Ferb's intro starts with "There's 104 days of summer vacation..."
"Disco Do-Over":
Dakota and Cavendish have to collect lawn gnomes that look just like the ones in Phineas and Ferb. One of them even comes directly from Drusselstein.
Doofenshmirtz has been chosen to be the judge in a roller disco dance competition Brigette and Martin signed up for, due to a popular video of him on the internet. Said video is the same embarassing video that had been leaked in "Tip of the Day".
By the end of the episode "The Ticking Clock", Victor Verliezer, stuck in a ball of chewing gum, gets flown towards the 28th Annual Subtitute Teacher Day meeting. The 27th one was held in "Summer Belongs To You", and features almost the exact same group of teachers (except for the last one, who was replaced by Ms. Baxter from Milo Murphy's Law episode "The Substitute").
When Doofenshmirtz's papers describing his unlucky experiences clogs up the school bus in "Milo's Shadow", he notes some of his experiences, including getting hit by a tin foil ball ("Rollercoaster"), and being tied to a birthday rocket ("Dude, We're Getting The Band Back Together!").
In "Adventure Buddies", when Doofenshmirtz describes himself as a third wheel, Scott responds that it's more like he (Scott) and Mildred are on a bicycle and Dr. D is on a unicycle. The same response as Candace gave in "The Baljeatles" when Stacey claimed to feel like a third wheel.
The Chicken Replace-Inator from "What a Croc!" (and later Phineas and Ferb The Movie: Candace Against the Universe) makes an appearance in "The Goulash Legacy", and a miniature version does in "Sphere and Loathing in Outer Space".
The trolley Milo and the gang use to break into the Museum in "The Undergrounders" bears a significant resemblance to California Adventure'sRed Car Trolley◊.
"Rooting For the Enemy":
Bradley unhappily greets Milo with, "Hello... Mi-lo," in a manner similar as between Jerry and Newman.
Bradley is about to sit with Melissa on the school bleachers until he spots Milo, then undergoes a series of convulsions that more than a few people have compared to Crocker from The Fairly OddParents!
Doctor Zone's origin heavily borrows from Superman's.
A segment from opening of The Dr. Zone Files resembles the opening of Doctor Who Series 8.
The Dr. Zone end credits include that the series was shot at "Balsawood Studios", a spoof of the famous Pinewood Studios in the U.K.
At one point in "A Christmas Peril", Cavendish exclaims "Oh my giddy uncle" in frustration, referencing the Second Doctor's catchphrase "Oh my giddy aunt!"
In "The Math Book" Milo, Melissa, and Zack walk through a cobwebby corridor before Milo has some Halloween decoration spiders on his shoulder which he calmly brushes off with a cord. Melissa and Zack suddenly have many more real spiders all over them. Even the background music is reminiscent of the Raiders scene.
In "Perchance to Sleepwalk", Dakota mentions a movie called Neptune Needs Women.
In "Fungus Among Us":
When Milo explains his favourite episode of Dr. Zone, a SpongeBob SquarePants-styled time card shows up saying "two hours later". It's even read in a flat French accent, like the show itself.
When it's decided to time travel to 1965, Dakota has an Imagine Spot of Rowan and Martin's Laugh-In, creeping out everyone else. (But he's thinking of the wrong year, as the series started in 1968.)
Derek’s backstory (surviving his race’s extinction by being removed from the timestream and subsequently planning to revive his race) is reminiscent of Doctor Who's Cult of Skaro, a group of Daleks.
The 70s-style funk song "How Do I Do It?" appears to be a straight up parody of Uptown Funk by Mark Ronson and Bruno Mars, complete with Milo, Melissa, Zack, Phineas and Ferb wearing the same getups from the music video.
"Picture Day" features two animal cameo characters: Recurring Raccoon, which may be a parody of Rocket Raccoon from Guardians of the Galaxy, and Zippy the world's fastest koala, a possible parody of Kwicky Koala.
In "Parks and Wreck", Milo mentions Hamilton H. County, the less popular brother of Jefferson G. County. When Principal Milder asks why she's never heard of him, Milo explains that "his enemies destroyed his rep and America forgot him."
The episode title "Sphere and Loathing in Outer Space" is a play on Fear and Loathing in Las Vegas, and the eponymous opening theme appears to be in a similar style of 1960s James Bond opening numbers.