These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Base Breaker: There are several: synthesists, gunslingers, and the magic-dead, technology-is-king region of Numeria are among them.
The encounter with Iomedae in Herald of the Ivory Labyrinth has become rather divisive.
That the setting includes direct Lovecraftian copypasta despite the fact it was stated the designers would not include Lovecraftian mythos.
Curse of the Crimson Throne: The followers of Zon-Kuthon, God of Envy, Pain, Darkness, and Loss tend to be a nasty bunch, with a penchant for torture and self-mutilation. Yet not a one of them—including quite possibly Zon-Kuthon himself—has ever come close to the level of atrocity perpetrated by Kazavon, Zon-Kuthon's one-time Champion. Essentially Vlad the Impaler in the form of a sixty foot Blue Dragon, Kazavon disguised himself as a human mercenary and offered to help the nation of Ustalav drive out the invading Orc hordes. Upon his victory, Kazavon set himself up as the dictator of the borderlands area, where he ruled with an iron fist, torturing to death all those who disagreed with him, including many of the soldiers who had served him faithfully up to that point. When his employer tried to rein him in, Kazavon flayed the man alive. He would go on to achieve truly special heights of depravity, holding torture parties, and orgies involving the undead, spreading his influence throughout the entire area, and having entire villages impaled for his entertainment. Kazavon was eventually killed by a party of heroes, but the madness didn't stop there. The pure evil of his soul contaminated his skeleton and threatened to resurrect him. The bones were crafted into seven Artifacts Of Doom and hidden throughout the country; contact with even one of them is enough to drive the wearer down a path of madness, murder, and ultimate self-destruction. When Queen Ileosa, Big Bad of the Adventure Path dons the crown, Kazavon influences her to murder her husband, turn Korvosa into a Police State, unleash a plague against the city's poorest citizens, and drain the lives of thousands in an effort to gain eternal youth (in reality, the spell will just resurrect Kazavon).
Second Darkness: Allevrah Azinrae was once an Elven cleric of Nethys, God of Magic, and a hero in the nation of Kyonin. That was before she, with the aid of the Demon Lord Abraxas, conceived of a plan to exterminate the drow. When the fellow members of her Government Conspiracy refused to go through with the plot, Allevrah murdered her critics, let her rage transform her into a drow, and fled to the drow capital of Zirnakayinn, where she murdered the matron of House Azinrae and took it over. Desiring revenge on Kyonin, Allevrah plans to drop a meteor on the capital; if successful this plan will wipe out Kyonin and trigger an ice age that will kill most life on the planet. After a failed attempt at using the city of Riddleport as a test target, Allevrah retreats to the Land of Black Blood below Kyonin, where she prepares to summon her meteor. She also allows her lover (who is terrified of her) to perform hideous experiments that reduce the victims to masses of screaming black liquid, cuts deals with an aboleth mind rapist and a neothelid, feeds prisoners to ropers, and orders her troglodyte henchman, Ornn, to eat a charda colony's children if they do not cooperate with her. Driven solely by hate, Allevrah shows just how far even the best person can fall.
Pathfinder's evil deities can be a bad lot, but none are quite as horrible as archdaemon and Horsewoman of War Szuriel. A former paladin, Szuriel became a conquering empress who had every member of her former faith crucified in revenge for her excommunication. Following her death, she became a daemon, and murdered her way to the top of Abaddon's hierarchy, eventually slaying the previous Horseman of War and taking his title. In her new rank, Szuriel represents war at its most terrible, celebrating societal breakdowns, scorched earth campaigns, and ethnic cleansing, and counting Insane Admirals, General Rippers, and Sociopathic Soldiers galore among her most devoted followers. Hiring out her daemons to those who pay the most, Szuriel inevitably turns on her employers, after forcing the campaign to degenerate to the point where mutual genocide is the only way it can end. Forging weapons in the heat of burning human souls, and revelling in violent excess, Szuriel demonstrates what happens when a Physical God adopts the mentality of the most sadistic Psycho for Hire.
Crazy Awesome: Cayden Cailean, in his mortal life as well as during his godhood.
Lamashtu towards Shelyn, who she wants to corrupt.
Everyone loves Shelyn, so most of the Evil Gods tend to like her like this.
Sarenrae and Asmodeus have a little of this going on; Inner Sea Gods even mentions their rivalry is a passionate one.
Fridge Brilliance: Why does Pathfinder invoke Lovecraft Lite despite being the Darker and Edgier counterpart to Dungeons & Dragons? Because it's only logical to do so! Most of the horror for Lovecraft's characters comes from the sheer shock in seeing such alien creatures and experiences, which so drastically contrast their understanding of realitynote arguably, Values Dissonance plays a big part in the horror, too. However, the inhabitants of Golarion — or, really, any D&D-ish setting — have a far, far broader view of reality than Victorian humans do. When your neighbor is a youthful girl who has outlived two generations of your family, your other neighbor is able to twist reality to his whims with some mumbo-jumbo and funny gestures, and your king could well be massive, nigh-immortal, immensely powerful dragon, something like a Mi-go doesn't stand out that much. The world is so full of strange and twisted lifeforms that creatures of the Mythos simply aren't any stranger than anything anyone's already seen. Add to that the fact that killing such creatures is bog-standard, and Mythosian monsters lose yet more of their power to scare the denizens of Golarian. By the standards of a basic Lovecraft hero, a Golarion adventure engages in Did You Just Punch Out Cthulhu? every time he cuts down a raging orc warrior or a drow or, heck, even a goblin.
Depending on who you ask, the 3.5 CoDzilla (overpowered "Cleric or Druid") problem has either been preserved or addressed, with both sides arguing that their claims are correct. Given that everything boils down to individual player preference and the skill of the GameMaster to arbitrate these things, its probably best to Agree to Disagree. However, most people agree that the problem at least has been toned down.
End-level spellcasters in general, unless you buff the CRAP out of your enemies' saves. Or give them spell resistance.
Or give them the stealth/dexterity to act first. Concentration checks to cast while taking damage is no longer a skill in pathfinder... while this means that you don't have to spend precious skill points to do it, it also means that there's no way to nullify it, or set up enough skill buffs that you'll automatically succeed. A rogue flanking a caster will make casting especially difficult, and fighters actually have a lot of options that make in a nightmare to try to cast against them within 30 feet.
The Synthesist Summoner archetype breaks the game so thoroughly that it's officially banned from organized play.
Some argue that it is no worse than the normal summoner or a Co Dzilla, it just interacts with the party in a way that makes the existing flaws obvious. A Co Dzilla can outshine the fighter too, but that is really all the Synthesist does, so they can't avoid it.
The entire Gunslinger class. Which is a full BAB ranged class (which automatically makes it more than powerful since Ranged full attacks are so much better than melee full attacks) that also targets Touch AC, which is almost universally the worst stat on most enemies and they add their DEX bonus to AC for free. Which no other class can do except for an expensive magic item ability for melee weapons only. Although not banned in PFS play, it is commonly banned in home campaigns.
Sarenrae's holy symbol features what would latter become Dark Souls's "Praise the Sun" gesture.
Zon-Kuthon's origin story is in several aspects a Darker and Edgier version of Nightmare Moon's.note One of a pair of good-aligned divine siblings encounters and is corrupted into a darkness-themed humanoid/equinoid abomination by a mysterious sinister force, is banished to another realm, and escapes their prison.
Iron Woobie: While the specifics have never been given, it has been stated that the goddess Desna's past has been shaped by tragedy and loss (including the murder of her closest friend and mentor), but she keeps on going without complaint.
Merisiel and Kyra, if the "Ask Merisiel" thread on Paizo's forums is to be believed. Apparently, if she could spend one night alone with any of her companions, it would be Kyra and what she would do... is not something that she would be allowed to say in polite company. All we've got is her line about how humans "can be super sexy and intriguing, especially when they worship Sarenrae and wear so much armor that you can't make out the details but just barely."
Merisiel: Kyra's still kinda a stick in the mud, but she's getting better at it. Slowly. Operation "loosen up the cute cleric" continues into its fourth year, in other words.
Merisiel: Best part about Kyra's healing magic? They're touch spells, and she's too kind-hearted to NOT heal someone who's actually hurt.
Kyra: By the Light of the Dawn, people, STOP encouraging her! I have enough problems keeping Valeros in line...
Merisiel (to Kyra): Kissy kissy!
LGBT Fanbase: Since the Rule 34, there's been a surprising degree of internet support for the Valeros/Imrijka pairing.
It's large in general thanks to the popularity of bisexuality in the setting — see Everyone Is Bi on the main page.
Many lesbian NPCs appear throughout the various modules.
At least two lesbian-transsexual couples (lesbian/bisexual woman, male-to-female transsexual) appear in the adventure paths; Anevia Tirablade (human) and Irabeth Tirablade (half-orc) note No, not siblings, they're married in Wrath of the Righteous, and Marislova (half-elf) and Jadrenka (changeling) in Reign of Winter.
Rescued from the Scrappy Heap: The developers sought to do this with some of the classic monsters in the splatbook Misfit Monsters Redeemed, specifically going for some of the most laughed-at monsters from the older editions of D&D, such as the Dire Corby, Wolf-in-sheep's-clothing, and the infamous Flumph (which is now a good-aligned extraplanar messenger warning adventurers about threats from beyond the stars).
Golarion Goblins, unlike most versions of D&D, are essentially pyromaniac psycho chibis. Even cuter in the expansion books, where they tend to dress up as other monsters and carry around big d20s.
Fungus Leshy as well. Most of the leshy are Ridiculously Cute Critters, but the fungus-based ones look like baby spawn of Shub-Niggurath.
Cacodaemons, the lowliest of all daemons, are essentially flying mouths with eyes. They want to eat your soul, but how do they look so huggable while doing it?
Similarly, quasits, which are the demon counterparts to imps and cacos. The one in the bestiary is trying to look evil, but the fact that it's standing next to a candle kinda ruins the effect and makes it look somewhat adorable.