Alan Moore really, really hates Harry Potter. His Top 10 spin-off fantasy mini-series Smax features a field trip from a wizard school being horribly killed by a dragon because of their teacher's recklessness (a reference to common fan criticisms of Hogwarts staff's casual attitude to dangerous creatures). The League of Extraordinary Gentlemen: Century turns into an incredibly vitriolic denunciation of Potter as artistically and politically reactionary, with Harry massacring the entire rest of the Potter cast, turning out to be literally The Antichrist, and finally getting killed by Mary Poppins.
Peter Grant in Rivers of London frequently uses Harry Potter as an analogy, such as comparing the Wizarding School his boss attended to Hogwarts, or calling a game where the players use magic to chuck tennis balls at each other "Pocket Quidditch". Whispers Underground opens with Snooping Little Kid Abigail looking for the Hogwarts Express. (That is, she's quick to explain, the train they used in the films. Not the actual Hogwarts Express, because it doesn't exist.)
Live Action TV
Supernatural had one episode where a female was being used as bait. She was nervous until encouraged to think of her favorite heroes. She picked Hermione and listed several facts about her before being told to focus.
The Big Bang Theory: In one episode Leonard reads the last book, and Sheldon and even Penny spoil several plot points for him.
In the Doctor Who episode "The Shakespeare Code" the Doctor mentions having cried reading the last book. The episode aired before Deathly Hallows was published. Additionally, Martha banishes the episode's villains with a spell ending "Expelliamus!".
In Agents of S.H.I.E.L.D., Lance Hunter explicitly compares most of the so-called "Real SHIELD" to Hufflepuff as a way of insulting them.
A season one episode has Skye refer to the SHIELD academy as "SHIELD Hogwarts."
In the pilot, a beleaguered Simmons says that she isn't Hermione.
In an episode of Rooster Teeth Shorts, it turns out that Joel was only halfway through on the book series before Matt spoiled it for him.
During The YoGPoD, when doing a musical quiz using iTunes and the "shuffle" feature, many of Lewis Brindley's answers are tracks from the audiobooks, causing Simon Lane to ask incredulously if he actually has any music on his computer.
At the start of the Minecraft series Magic Police, Duncan Jones and Sjin start discussing the series, only for one of the duo to mistake the spell "crucio" for "crucify", which causes them to remark that the series would have taken a darker turn if that had been the case.
Cards Against Humanity has at least three cards relating to the franchise. The first is "Next from JK Rowling: Harry Potter and the Chamber Of _____", while another is "Daniel Radcliffe's delicious arsehole" and a third is about "Harry Potter Erotica".
When the Simpsons travel to Britain, Lisa meets Ms Rowling and compliments her on bringing the whole generation of children to reading.
A launch of new Angelica Button book (its final installment) is a clear reference and parody of the Harry Potter craze, complete with arguments whether the costumes refer to the book or the film.
In another episode, Ned Flanders reads a book to Rod and Todd and says that Harry and his friends "went straight to Hell for practicing witchcraft" before throwing the book in the fireplace.
During "Homer and Ned's Hail Mary Pass", Marge is busy criticising Ned's Bible films as too bloody and too gory, while also missing out many of the Bible's sweeter moments. He sarcastically asks if she'd rather see films about "a liberal European wizard school"; three guesses as to which series he is referring.