The most obscure example would be Bubsy, whose catch phrase was "What could possibly go wrong?!"...which became Timmy's catchphrase. Also considered a Take That! since this line is delivered in the most wooden, cliche way possible.
Another in which Timmy creates a male version of Vicky for her to fall in love with, at the end of the episode Ricky goes off with Crocker's mom (after a dating site mishap) and Vicky exclaims "Ricky, don't lose my number! You don't have to call nobody else! Send it off in a letter to yourself!" a line from "Rikki Don't Lose That Number" by Steely Dan.
Dr. Mindbender was an orthodontist before joining COBRA, and his real name was "Dr. Bender".
In one episode where Timmy goes to tour his dad's workplace (with an obligatory Chocolate Factory spoof to boot), Mr. Turner gushes about how he's his boss's favorite employee to Timmy. His boss responds to this with a scream of "HOMER!" "—Uh, it's Turner, sir."
To AC/DC in "Light's Out," at the end, when Timmy denies that he was scared of Cosmo as Wanda in their 'Scardey Fairies' form, Wanda poofs it back to complete darkness with the poof saying 'Back in Black' and then back to light with the poof saying "Let There Be Light."
At the beginning, Timmy recreates the famous scene of Neo dodging bullets from The Matrix
When Cosmo and Wanda are using their magic to act as multiple tv stations as she switches through them, one them goes to "Cosmo!" with a surprisingly similar jingle. "It's a show about nothing! ... How do we know when its over?" The gag also works considering that Kramer's first name is revealed to be Cosmo. At another point, they recreate I Love Lucy
"I Was a Teenage Blowfly" (from "Fly Boy") stars Dash Baxter from Danny Phantom.
In "The Secret Origin of Denzel Crocker", Timmy decides that he has to go back in time further to see why Crocker is so miserable, and ends up in the 1980s. Seconds before he arrives there, we see the iconic DeLorean time machine from Back to the Future leaving a pair of fire trails behind.
"Odd Odd West" has one of the kids dressed in Lucky Luke style.
Competing for the most obscure reference: The Flash (?) expy in "Power Pals" is named Joan Jet.
Cosmo as Braveheart in "Homewrecking". (Episode contains also a possible Shining reference but that could be a generically Ax-Crazy Vicky.)
The Monster Hunter at the end of "No Substitute For Crazy". Fairy Wiki says it's an obvious parody of van Helsing, but a) which of them? b) Harry exists c) so does Geralt, so a Word of God would be helpful.