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.
YMMV: Deadly Rooms of Death
Anticlimax Boss: First Archivist in The Second Sky. Despite being the main antagonist, he's fought halfway through in a short and not especially difficult level.
Breather Level: The Second Sky has a few. "Chronometric Ruins" is deliberately toned down, as it introduces a potentially confusing new mechanic, the temporal split token. "Caught in an Eddy" gives the player a chance to recover after some extremely hard levels, and allows them to explore the other surface. "The Scorching Path" is a breather level... for no particular reason.
Journey to Rooted Hold's music is all excellent, but particular stand-outs are "Brood" and "Uncovered".
"The Architect's Oath", the title screen theme of Journey to Rooted Hold, with a stunning harpsichord instrumental section.
The Second Sky has a number of pieces by Emmett Plant that play during story segments. Particularly awesome tunes include "Within These Swingin' Halls" (Halph's theme), "Waltz Recombinant" (First Archivist's theme), "An Architect's Dream of Geometry" (the Farrow Child's theme) and "A Sympathetic Bartendry" (Tendry's theme).
Goddamned Bats: Anything in the hands of a competent architect. Wraithwings typically get the most hatred, though, since they can fly, will run away from the player if alone (typically over pits) but in hordes, will swarm the player in a hard-to-predict fashion (since their movement is dependent upon the location of other wraithwings and the movement order of the whole horde).
Consensus says that Levels 8 and 13 of King Dugan's Dungeon definitely fall into this state, and there are also particularly nasty rooms spread throughout the series.
In Journey to Rooted Hold, it's Level 22, an exhausting run through several large horde rooms. Most of these don't require normal completion (i.e. killing all monsters in the same visit) but just getting through them so you can reach a different entrance and set off bombs. Yet somehow, just getting through these rooms is harder than completing rooms on other levels!
Some user-made holds are infamously difficult. Gigantic Jewel Lost comes to mind.
The official level set Beethro's Teacher consists entirely of Those Six Levels.
The Second Sky brings several. Shattered Mine, Temporal Anomaly, Experiment of Ages, Rapid Fortification, and Mother of All Roaches all fall under this category.
That One Puzzle: Each game has one or more rooms that have acquired particular infamy. This list uses DROD's usual coordinate system, e.g. "1E" means the room once east of the level entrance.
King Dugan's Dungeon: Eighth Level, 7S3E. Just mention "three tar mothers" to any DROD veteran and they'll instantly know which room you mean.
Journey to Rooted Hold: Sixteenth Level, 2S2E. A grid of obstacles interlaced with rock golems — enemies that leave piles of rock when you kill them. It's extremely difficult to avoid these clogging up the grid.
The City Beneath: Abyssian Fortress, 2S. Tarstuff clearing on a very small platform.
The Second Sky has quite a few. Shattered Mine 1E, Eye of the Storm 1E, WBCEND/Caber Testing Area 3S1E, and Lemming Beach 2S4E have all stumped many players.