Lovecraftian monsters such as Shoggoths, Deep Ones and even Great C'thlhu himself should be familiar to consumers of fantastical media. Whether in games (Call of C'thulhu, Trail of C'thulhu,) movies (The Dunwich Horror, Dagon) or in any of the many new stories set within the Lovecraft Mythos, new authors have worked to bring Lovecraft's visions to the modern age. Some of these products are quite good, but if I may offer my opinion, gamers and creators who want to truly tap into the Lovecraftian might want to venture off the path established by the man himself.
What do I mean by this? Well, C'thulhu and company were originally meant to be scary because they were strange and unfathomable. When you can buy plush toys of said monsters, that aura of the strange and unfathomable decreases significantly (not that I don't love some of those toys myself.) Lovecraft's stories were also full of rather dated (to put it kindly) anxieties that don't quite work for the modern horror afficianado; immigrants and their descendants have established that we're not going away any time soon, and tentacled monsters have become so commonplace in SF art that, far from boggling the mind, they inspire jokes about Japanese pornography.
There is still some terror and excitement to be had in traditional Lovecraftian fare, but if the above problems are too much for you, you can still enjoy media that take H.P.'s favorite concepts without using his specific creatures or stories. Consider Buffy the Vampire Slayer. In that television show, demons from other dimensions once ruled the earth, and their lines (and blood) mingled with those of humans to create vampires, humanoid abominations intent on reclaiming the Earth for their dark gods. That's almost a dead ringer for the plot of Shadow over Innsmouth, except that extraordinary humans such as Buffy and her friends are capable of fighting and defeating the monsters.
In his book Danse Macabre, Stephen King stated that he considered Alien to be, at heart, a supernatural Lovecraftian film. In this case, humans travel the stars and find the ancient gods rather than the other way around, but the end results are the same. Alien even shares the Freudian sexual terror at the heart of many Lovecraft stories, albiet with phallic and toothy rather than vaginal and squishy monsters. At the end of the first movie, heroine Ripley is in much the same position as the heroic boat captain of Call of C'thulhu- she has used her ship to save herself from the alien, but can there ever be a true victory over such a creature, or is she only delaying the inevitable?
Lovecraftian creatures don't even have to be malevolent to be creepy. The ghoulish humor of the film The Nightmare Before Christmas, the Addams Family television show, and the game Monsters and Other Childish Things relies on the idea of aberrant entities being merely curious about humanity, and driving people mad with what they consider harmless fun or even attempts to help. If that sounds like legends of the Fair Folk, you'd be right; remember that the word "eldritch" originally meant "elvish", and you'll see the routes of Lovecraft's aliens even in fairy tales.
Especially interesting is when you find Lovecraftian elements in stories that aren't meant to be horror-related at all. Oscar Wilde's short story The Birthday of the Infanta shares exactly the same plot twist as Lovecraft's The Outsider, only with a different pre-reveal mood. The Indiana Jones films show godly artifacts that bend and distort reality, best kept away from humanity's use for fear of the damage they could cause. Moreover, one of the quintessential American heroes has a backstory that, with only a few tweaks, could describe Dunwich's Wilbur Whateley.
The child of a dead species from a distant planet, he passes as human but is fundamentally not. His small town knew he was strange, but never guessed what he truly was. This alien boy eventually traveled to the frozen north, where, buried in the ice, he found the legacy of his parentage, and brought it back with him when he came back to the world of humanity. Human scientists can slow him down, but they will never truly be able to destroy him, or even comprehend what he is.
Superman is Earth's champion, for which we are very lucky. Like horror itself, the Lovecraftian can be found almost anywhere, and it only takes a little bit of reframing to bring it out.