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!" 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."
The Giant Fairy Storage in "Escape from Unwish Island." Just to name a few, some of the people who have lockers are Walt Disney, P. Diddy, Duran Duran, Carrot Top, Milli and Vanilli, and some people working on the show itself just to name a few. It's like a goldmine of Shout Outs.
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.