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Children of the Void introduces two types of alien monsters, the parasitic akatas and the plantlike moonflowers. The former are inspired by the Xenomorphs from the Alien movies, while the moonflowers take their inspiration from The Day of the Triffids and Little Shop of Horrors.
The cover of Seeker of Secrets features an adventurer engaging in the industry-wide gag of pulling ruby eyes out of grinning idols as a tribute to one of the first Dungeons and Dragons covers.
The campaign setting timeline mentions that a large forest was trampled by "the Slor".
Classic Horrors Revisited tells us that gargoyles' appearance adapts to their environment over time. One particular tribe has been living in a graveyard so long that they look like angel statues, and they've picked up a curse that causes them to freeze into immobility when anyone looks at them. Just don't bli—
The monster designs in Bestiary II are loaded with shout-outs. Obvious examples are the Arbiter (a legless Modron), Cacodaemon (a miniature of the Doom version), and Soulbound Doll (the Zuni fetish from Trilogy of Terror and the Maidens from Rozen Maiden).
Speaking of ol' HPL, Paizo's gone beyond the subtlety of the Shout-Out and directly printed in several of their materials just how wicked sweet and totally awesome the Cthulhu Mythos is, and by the way you should check out Chaosium's Call of Cthulhu game. The most explicit examples include the adventures Carrion Hill and Wake of the Watcher, inspired primarily by "The Dunwich Horror" and "A Shadow Over Innsmouth" respectively, Bestiary II which features the Spiders of Leng, the Hounds of Tindalos, Shoggoths and Lovecraft-style Ghasts, and Faiths of Corruption which includes cults of the Great Old Ones. As both a capstone reference and campaign-ending encounter, Wake of the Watcher includes stats for a Star-Spawn of Cthulhu.
The sourcebook for Andoran mentions some of its smaller but notable communities, including the towns of Claes and Triela.
Two of the peaks in the Five Kings Mountains are named Mounts Langley and Soryu.
The sourcebook Princes of Darkness, focusing on using devils in a campaign, features a magic item called a bilious talisman, which strongly resembles the Behelit from Berserk.
One reference liable to go over the heads of modern gamers - the Holy Gun archetype in Ultimate Combat gains firearm-using feats from a class feature called Have Gun. If you couldn't guess, this is for a variant paladin.
The Kellid and Shoanti human ethnicities are strongly inspired by the Cimmerians and Picts, respectively, from Robert E. Howard's mythos. (The Shoanti have a little Native American thrown in... but then, so did Howard's Picts.)
There are several different kinds of gremlin in Pathfinder, but one in particular, the jinkin, is based on the movie Gremlins.
The underwater "gillmen" are a clear Shout-Out to the Atlanteans of Marvel and DC Comics, like the Sub-Mariner (on whom their illustration is strongly based) and Aquaman.
The Red Planet of Akiton (initially mentioned in Children of the Void and further detailed in Distant Worlds), with its giant four-armed warriors, is clearly an homage to Edgar Rice Burroughs's John Carter of Mars novels.