Worm: Already mentioned in this thread but it is complete, well written, and has an AWESOME premise. TL;DR super powers are somewhat common, world sees them as heroes/villains but it's much more accurate to consider them rival gangs--they're all assholes abusing their powers and the "heroes" are closer to "taking over the world" than any villain is. Protagonist tries to ride both sides of the fence and do actual good work but with a power considered both weak and villainous (She controls worms/roaches/spiders/flies) there are lots of misunderstandings. That power never changes (until the VERY end...), but her innovative usage of it upgrades her from a "rank F" to a "rank SSS+" over time.
The Gods are Bastards: Again, well written with an interesting concept. TL;DR Gods exist, most have a religion, and many call a paladin to serve as their avatar on earth. The series starts with Avei's new paladin being told by her goddess to "go to hogwarts" essentially... which is headed by the most powerful mage on earth who has talked to/fought with/made bitches of/... almost every god in existence and who (for the most part) thinks they're all a bunch of insufferable little shits. She quickly realizes once she's there that despite being a paladin she's just "another bright student" at "not hogwarts" and that she doesn't really fit in because she's kind of a stuck-up bitch because of her dogmatic approach to religion. Very interesting take on the consequences of "the D&D premise of religion" (IE there are many competing religions, and all of them are verifiable fact).
Trash of the Count's Family: "Almost isekai" in which the MC is transported into a novel he's read about half of as a "throw away" side character that gets rofl-stomped by the novel's hero in like the first chapter. Eschewing the normal tropes of "I'll become the hero/villain/most powerful person ever/..." throughout the entire novel his goal is just to get the Hero to move on with his life and the business of saving the world so he can live the life he was born into... that of an insanely rich and pampered son of an influential duke. Unfortunately since he's constantly having to bend and manipulate things to keep the characters on the path of their "book arcs" so the whole world doesn't go to hell he is in-universe seen as this master puppet-master and the "hero behind the hero" which he fights desperately to avoid.
Log Horizon: They made a decent anime off of this one so could also check that out... but I remember reading the LN on Baka-Tsuki way before it came out and being pretty impressed. Basically Sword Art Online premise but "death is mostly meaningless" while rape, slavery, and "CC effects" like mind control or charm are fucking horrifying. Forming stable governments, trade relations, and the creation of "modern technology" within the virtual universe are immensely important to the plot while leveling and adventuring are mostly after-thoughts.
WAY down after those I'd consider The Legendary Moonlight Sculptor (royalroad was initially just a host for fanfiction based off this influential work), Korean works by "Toika", Chinese works by "Er Gen", and "Tang jia san shao", and English works by SenescentSoul, Vihyungrang, Andur, and Rhaegar.