Saturday Night Live: An infamous TV Funhouse sketch from Season 23 is about a song from Conspiracy Theory Rock! about a "Media-opoly".
They also had a regular skit spoofing how Obama's "Executive Order" would do things much faster than the time it takes for a Bill to become a Law, featuring Kenan Thompson as Bill.
MADtv occasionally ran "Public Schoolhouse Rock," which poked fun at and exaggerated troubles often faced in overcrowded urban community schools including corporately-backed and unhealthy school lunches, unsafe hallways, unwilling classroom students and uncaring substitute teachers.
American Dad!: In "Stanny Slickers II: The Legend of Ollie's Gold", Stan sings a SHR-styled song about Oliver North and his role in the Iran-Contra scandal.
BoJack Horseman: In "See Mr. Peanutbutter Run", the scene where Katrina drafts a pork-filled bill to make the gubernatorial race decided by a skiing competition is styled like Schoolhouse Rock.
Drawn Together: In "Foxxy vs. The Board of Education", the titular board is drawn like a Schoolhouse Rock character. Later on, when Foxxy prevents a load of grape-flavored pencils from being delivered to schools, they were being stored in train cars from "Conjunction Junction."
A sketch from "I'm Trapped" features a SHR-like song about homonyms and how you can use them to get away with saying offensive words.
A sketch from "Robot Fight Accident" features the Schoolhouse Rock characters taking a more confrontational approach to basic learning.
The Simpsons: In "The Day the Violence Died", The Itchy & Scratchy Show is replaced by a parody of Schoolhouse Rock; the song is a spoof of "I'm Just a Bill" and depicts the passing of a law banning the burning of American flags.