Cthulu is a pretty cool monster... I mean, look at him:
Depending on your personality, you just don't want to make that guy angry, or you want to attack him and take him down. Either way, he's awesome. Which is why it isn't too surprising that he's all over the place in pop culture.
The first printing of the original Dungeons & Dragons Deities & Demigods book included an entire chapter on Cthulu and his mythos. Unfortunately for them, Cthulu was copyrighted and they had to remove him from subsequent editions.
Magic: The Gathering includes a group of beings called the Eldrazi, who are heavily influenced by Cthulu in description and power.
Several video games, including Quake, Lost Souls, and World of Warcraft include either direct references to Cthulu or characters (usually boss types) that are clearly modeled on him and the other old gods. Did you know that you can summon Cthulu in Scribblenauts? Seriously... try it; it's adorable.
Lots of bands have songs either explicitly about or influenced by Cthulu: Gwar ("Horror of Yig"), Cradle of Filth ("Cthulu Dawn"), Blue Oyster Cult ("The Old Gods Return"), Deadmau5 ("Cthulu Sleeps"), Metallica ("All Nightmare Long" and "The Call of Ktulu")... there's even a band called H. P. Lovecraft.
He shows up in other books, too. Eoin Colfer slid him into the final installment of Douglas Adams' Hitchhiker's Guide to the Galaxy six-book "trilogy" where he was interviewing for a position as god of a small planet. Terry Pratchett makes several references throughout the Discworld series, and Neil Gaiman has written a short story called "I, Cthulu" that is meant to be an autobiography of the beast. (He wrote about him again in "A Study in Emerald," which is like a Sherlock Holmes and Lovecraft mashup.)
Cthulu has also shown up on television: Scooby-Doo! Mystery Incorporated, The Grim Adventures of Billy and Mandy, Supernatural, True Detective, several episodes of Dark Shadows, and (pictured above) South Park have all incorporated Cthulu or parts of his mythos.