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.
The Lair, depending on your build. While it contains some powerful threats of its own, a character that hasn't been too fond of Dungeon Bypass typically has no problem clearing the branch as soon as they find it. The Lair's sub-branches are far from being easy, though.
The dungeon levels between The Lair and The Vaults typically don't progress in difficulty as fast as the character gains power, making them fairly easy to clear. Further emphasized as many players clear The Lair and Orcish Mines before going that deep.
The Ecumenical Temple, an early area which contains nothing but a bunch of altars, so your character can choose a god. No enemies will ever spawn here (though some enemies can follow you in) which is why many players use the temple for resting and for keeping their stash. (Similarly some players keep a stash in The Lair, since none of the creatures that spawn there can use items.)
Worst of all was The Hive, a Breather Level deemed so bad that it was removed entirely from later versions of the game. It consisted entirely of killer bees and killer bee larvae, which are deadly early in the game but can be dealt with trivially if you put it off for later (at least until you found some way of reliably resisting poison), and contained an unbalancingly-high quantity of not just free permafood that all characters could eat but also the best food item in the game (which doubles as a potion of restore abilities).
Character Alignment: Many gods the player can choose to worship follow a strict alignment, which dictates how the player pleases (or displeases) them. They will often be tagged as such in the game.
Lawful Good: Zin, the god of law, who abhors evil and chaos. Mutations and other chaotic acts displease him. The Shining One, as well, who wants followers to fight honorably, i.e. not using poison or sneak attacks. Both gods detest the use of evil artifacts such as demon weapons, and evil magic such as Necromancy. Together with Elyvilon, they form the "Good god" alliance.
Neutral Good: Elyvilon, the god of pacifism. The only god in the game to endorse pacifism, she smiles on followers who pacify monsters rather than murder them. She also detests evil equipment and magic, as well.
True Neutral: Okawaru, god of battle. He doesn't care what you do so long as you continue to battle monsters in his name, but he frowns on killing allied creatures, even accidentally. Also Trog, god of slaughter, who doesn't give a damn what you do, so long as you regularly kill stuff and don't use spells; and Sif Muna, who wants you to seek magical knowledge, but doesn't care what you use it for.
Chaotic Neutral: Xom, who doesn't give a damn about you other than as a source of entertainment. Jivya, as well, who just wants to devour everything, but appreciates your contribution to that goal. These two gods are explicitly tagged as chaotic in the game. Zin hates them, but they don't seem to care much about him. There's also Nemelex Xobeh, the trickster god who encourages followers to gamble.
Lawful Evil: Yredelemnul, the dark analogue to the Shining One. He has the most stringent guidelines of the Evil gods, but grants you powerful undead followers if you stick to them.
Neutral Evil: Beogh, the racist and violent god of the orcs, who is tagged as evil by the game. Kikubaaqudgha, the demon-god of Necromancy, is also tagged as evil.
Chaotic Evil: Makhleb, the only designated chaotic and evil god in the game, Makhleb revels in indiscriminate destruction, accepting all kills, be they evil or good monsters. He will grant you destructive powers if you further his goal, but the powerful demons he lets you summon may turn on you. Lugonu is this as well, being the god of the chaotic Abyss, tagged as evil in-game, and granting powers dedicated to corrupting the order of the dungeon.
Orc priests. They can smite even the toughest early-level adventurer to death in only a couple hits, as soon as they see him, no matter who or what is in between - and they usually come with simple orc meat shields that you must hack through before getting to them, all the while they are smiting at you.
Centaurs. Combine their powerful bows with their high speed and you have an enemy that deals high damage from a distance and is almost impossible to escape from. You can hide behind a corner to lure them into melee, but get caught in the open (without the Repel Missiles spell) and you're toast.
Unseen horrors. They're fast enough to move in, hit you, and back away all in a single turn, and when they hit they can hit hard. Oh yeah, and they're invisible. Their invisibility is particularly nasty for lightly armored characters who tend to focus on evasion, as the evasion stat is ignored by invisible foes. And their random movement makes them the only invisible enemy in the game where you can't usually guess what tile they're standing on even right after they hit you.
Spiny frogs are the bane of many casters, particularly because of their poison resistance that makes them immune to the confusion spell "mephitic cloud." Running faster than you doesn't hurt their case.
Any sort of higher demon, but there are a few specifics:
Executioners are tier 1 demons (marked in the ASCII version of the game by the number "1") with super speed, which they like to boost even further with the haste spell. Once that's done they'll zip into melee combat and proceed to hit you like a freight train, often multiple times in a single turn.
Brimstone Fiends, Ice Fiends, and Shadow Fiends are all tier 1 demons most reviled for knowing (and loving to abuse) the spell Torment, which cuts your current HP in half with every use and is unresistable for most characters. While all monsters who know Torment are bad, Fiends up the ante by adding other nasty attack spells plus summoning hordes of minions. Shadow Fiends are perhaps the worst since they have the spell Dispel Undead, which deals massive damage to undead characters, who incidentally are the only ones able to reliably resist Torment.
The tier 3 demon Neqoxec also qualifies. Though somewhat weak, neqoxecs know (and love to spam) the spell Polymorph Other which, when used against the player always gives negative mutations. It's possible to resist this effect with certain equipment, but the neqoxec's status as a mid-level summon means players may end up facing them before they're ready.
Many Enemy Summoner foes are considered demonic spiders as well, including deep elf summoners and orc sorcerers, both of which rarely do battle without first calling in a dozen or so various demons. Vampires fit in this category as well (until version 0.12 when this ability will be removed) thanks to their tendency to flood the room with rats and bats the second they spot you.
Before they got nerfed, electric eels were this. They would appear in large schools in every body of water, fire painful bolts of lightning at you from across the room, and then dive underwater as soon as you got close. Fortunately they got a nerf at some point (the Crawl Wiki doesn't have the version number); they still fire bolts of lightning, but those bolts are much less damaging, the eels themselves are much less common, and they now only dive underwater if at critical health.
Game Breaker: The Storm spells, especially Fire Storm. Both spells deal damage comparable with Crystal Spear to multiple enemies, both are partially irresistible, and both leave damaging clouds behind. Fire Storm takes it further by having Smite-targeting (if you can see something, you can hit it, regardless of what's in the way) and summons fire vortices to distract survivors. If you worship Vehumet and wield a staff of energy/cast Necromutation, then you can cast it for free.
Nemelex Xobeh also qualifies if you know what you are doing. The legendary versions of his decks, along with high piety, a decent evocation skill, and liberal use of his gifted abilities essentially turn any PC (even purely melee focused characters) into an epic level mage. Capable of summoning dozens of creatures, in combat, with a zero chance of being hostile for a paltry 2 mana or blasting several of the strongest spells in the game better than an equal level wizard could. Plus powers possessed no where else in the game, such as the ability to create food out of nothing. On top of all this old Nemelex has a grand total of one real rule (using combat oriented cards when there's no one hostile around), meaning the only real way to get excommunicated is to stand around for tens of thousands of turns with out sacrificing anything to him or using cards in combat. Something a player is never going to do.
True of Crawl's bats. They barely even hurt you, but can hit multiple times in a turn, and have so much evasion they're hard to kill. Most annoying is that they're so fast they can move toward you, hit you, and move out of reach in one turn, meaning that you can't melee them unless you make some odd moves. Potentially deadly in the early game if you're unlucky, mildly irritating afterwards.
Later on you'll also run into Unseen Horrors, which are just like bats except they actually have decent attack and HP. Oh yeah, and they're invisible. (See Demonic Spiders, above.)
Ugly things and slime creatures later on in the Dungeon. Both always appear in packs, absorb a good chunk of damage before dying and flee when wounded. Ugly things also are slightly faster than most PCs and have randomly branded attacks (including all three brands that are capable of damage equipment and one that stops you from healing for a while) and resistances which randomly shift while in a group. Slime creatures, meanwhile have an incredibly annoying habit of fleeing and coming back within seconds, having completely regenerated in the process, and will merge into much more powerful brutes if you try to fight them one at a time in a corridor.
Crimson Imps (or just "Imps" in earlier versions) have three really nasty abilities: high evasion which makes them difficult to hit, the tendency to blink (short range teleport) a lot, and lightning-fast regeneration. Add to that they resist damage just like other demons while appearing at a point in the game before the player is likely to have strong enough weapons to overcome said resistance. Fortunately they deal very little damage, meaning they're generally a minor annoyance to distract you from more dangerous enemies. Unfortunately, they can pick up and use weapons on the ground just like you can. If they pick up something dangerous enough (like a good enchanted sword or a wand, or the bow left behind by a centaur) they can become Demonic Spiders with ease.
Another common killer of early characters is the not-so-humble adder. They're much faster than you, poisonous, have more health than most monsters during the first few levels and can appear on the second level of the dungeon. By that point you're unlikely to have a potion of curing identified, or any items that can help you escape, and usually have so little health that you'll be forced to start trying out random potions to survive if bitten more than once.
Memetic Badass: From the "Foolproof Plan for Winning Crawl" flowchart:
"Did you find something to kill? -> Is it Sigmund? -> You poor bastard."
Nightmare Fuel: If you have a good imagination, there could be plenty. Using Animate skeleton on a fresh corpse is one such case ("Before your eyes, flesh is ripped from the corpse!"). Another one is when you make an enemy bleed with your sharp claws and they proceed to run around the dungeon painting it red.
That One Boss: Crawl has enough for all stages of gameplay. Lucky characters may even live to encounter them all!
Sigmund is a human wizard notorious for killing off a lot of early level characters; he wields a scythe, which at this point in the game is a powerful weapon, can become invisible, casts confuse on the player and throws fire. Most players will want to avoid or escape him if they meet him, unless they have an edge, like a wand or potion.
Grinder is another early game That One Boss. He's a shadow imp who can paralyze the player and cast a nasty pain attack. Grinder typically appears just a bit later than Sigmund, and a popular joke among fans is that the two have a rivalry going on to see who can claim the lives of more newbies.
Nessos the centaur. Even normal centaurs are fairly bad because of their speed and ranged attack, but Nessos is even worse thanks to his unique ability. Ordinarily if an arrow has an enchantment it overrides that of the bow that fires it. Nessos ignores this rule, gaining the ability to fire flaming toxic arrows. Couple that with his liberal use of the spell Blink (which makes luring him into melee all but impossible) and he's easily one of the most dangerous mid-game uniques.
Maurice. A thief that'll haste himself, turn invisible, then sneak up to you and yoink your stuff. Losing your stuff is bad enough (though you will get it back if you can kill him) but depending on what he manages to get from you he can become extremely powerful. If he grabs a potion of healing he can be back to full health in a second. If he grabs a powerful enough wand then bend over and kiss your ass goodbye.
Mara is another late-game threat, appearing around the same time as Mennas. Not only does he have a dangerous spell list and the tendency to spawn with a decent weapon, he can conjure up illusions of himself, which are just as nasty, blink and teleport around, and create an illusion of the player, which is just as dangerous as the player is. Are you powerful enough to casually sling Fire Storms around? Your illusory self will be too!
That One Level: While all of Crawl could qualify for some people, there are specific examples:
Hell, which also qualifies as Bonus Level Of Hell, as befits its name. To even enter you need to kill the archdemon Geryon, who almost qualifies as a That One Boss thanks to his Enemy Summoner nature. Once he's down you have your pick of four equally lethal regions: the iron city of Dis, the fiery Gehenna, the undead-filled Tartarus, and the icy Cocytus. Each region is filled with hordes of demons, including large numbers of tier 1 and tier 2 demons, and is guarded by a powerful unique archdemon down at the very bottom. While that's bad enough, what really qualifies Hell for That One Level status is the Mystical Force, a vaguely explained... well, mystical force that regularly (every twenty turns or so) does some random bad thing to you. If you're lucky it'll only decide to confuse you (probably while you're standing right next to lava and/or in combat). If you're unlucky it'll decide to blast you with massive unresistable damage, stat drain you to death, or summon a tier 1 demon right next to you while you're trying to rest.
Followers of the god of order, Zin, will be granted (not infallible) protection against Hell's mystical force which makes them among the most suited to taking on this level, but even they have to be very careful of the demons and other monsters here.
The Tomb isn't quite as bad as Hell, but it's still considered to be by far one of the most hazardous of the game's many side areas. It's an undead-themed branch with an Egyptian flavor to it, meaning lots of traps and lots of mummies, most of which will spend their time either smiting you, spamming Torment, or summoning demons. Even characters specifically equipped for fighting undead still have to beware, as killing a mummy provokes a death curse, which might drop your stats, make your flesh rot off, hit you with a Pain spell for massive damage, or even summon powerful tier 2 demons to eat your soul.
The endgame, after collecting the Orb of Zot and you're ascending back toward the surface. You'd expect an easy return since you've already cleared all the floors, right? Wrong! First, while holding the Orb of Zot your stealth is decreased drastically which can be very damaging for certain characters. Add to that, teleportation takes a lot longer to take effect, and the duration of magical contamination is greatly extended. What's more, the game will spawn all new enemies to attack you, drawn from the Hell and Pandemonium lists. This includes Pandemonium Lords, which are the strongest non-unique enemies in the game and ordinarily only appear at a rate of one or less per floor in the demon plane of Pandemonium, but during the ascent you can fight multiples per floor, or even 2 or more at once.
In keeping with the apparently masochistic nature of Crawl players, one somewhat popular Self-Imposed Challenge involves waiting until the ascent to clear the Tomb, thereby having to deal with all of the Tomb's normal hazards, as well as the massively powerful demons summoned by the Orb. (The challenge would involve clearing the four regions of Hell, but once the Orb is picked up all of the branches of Hell are sealed.)