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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.
Demonic Spiders: The Wendigos are broken. They may die easily, but they shoot tons of ice balls that take out half your life if they hit you. And god forbid you play the highest difficulty (they shoot twice as fast). At least they only appear in a few levels.
Cue the Ice Hold in Deathkings of the Dark Citadel, a stage populated by nothing but Wendigos.
The Fighter likely has the biggest problem handling them, due to lacking any good ranged weapons on the first hub (which is where you encounter 90% of them). While you'd expect the Mage's second weapon to be ineffective against them, luckily it still harms them just fine.
Slaughtaurs come dangerously close. They look exactly like Centaurs, except they can fire projectiles from their shields. Which means the first frame of their firing animation looks just like their blocking pose. And combined with the fact that they fire almost instantly after assuming the position, this means that it's very difficult to beat even a single slaughtaur - let alone a horde of them - without taking at least one cheap shot.
Hexen II gives you the skull wizards and shadow wizards who like to teleport behind your back, blast you and then teleport away when you return fire, only to repeat the whole thing again.
Also in Hexen II are the were-jaguars and were-panthers, who take a ton of hits to kill, shred your HP on mere physical contact and can occasionally close the distance between you really quickly by leaping forward. Especially tough if you're a paladin and don't have any green mana for your axe or the Purifier, meaning you have to go in and deal with them in melee combat (and they're pretty good at dodging melee attacks.)
Quite possibly the Cleric's Wraith Verge: It is very easy to use and ammo tends to be plentiful enough to enable it's use quite often (it also helps that Harder Than Hard increases ammo pickups by 50%). Spamming it on the final boss will defeat him (and his army of Mooks) with relative ease if one knows the fight mechanics well. In multiplayer deathmatch, firing it upon another player forces them to either attempt to reflect the ghosts back with a "Disc of Repulsion" or retreat to avoid fatal damage.
The Heresiarch, an otherwise drawn-out boss battle, can be finished with ease by stun locking him as the Cleric, using Gas Flechettes. He is supposed to have an invulnerability phase, but this ignores all invulnerabilities.
Goddamned Bats: Centaurs/Slaughtaurs. They're everywhere and they have shields which make them invincible for a short time after every hit. They really aren't that dangerous, but certain classes' weapons (read: Cleric) make them take forever to kill.
They also reflect non-Hit Scan projectiles when they block. So when you're fighting a horde of them, be careful with your Infinity Plus One Weapon that you don't accidentally take the projectile right in the face afterwards.
Fortunately, the Cleric has the Wraithverge in his arsenal and that's a kill that a shield can't block. Granted, it sucks up a lot of mana, but if you can get the centaurs to cluster, one shot will take out a good chunk of their numbers.
Ways before that, Cleric can dispatch the Centaurs pretty easily with poisonous flechettes.
Slaughtaurs are also indistinguishable from Centaurs until they start shooting projectiles out of their shields at you.
Not only this, Mage's lightning spell helps same way. A LOT.
Remember those annoying gargoyles from Heretic? Well now they're called Afrits, their fireballs do more damage, they shoot a lot more of them, and they can dodge.
Now take those Afrits, give them one explosive fireball instead of a series of them that does even more damage, exchange the dodging ability with added toughness, and have them intermittently respawn wherever they appear. Now you have Reivers.
Hexen II has the flying imps who are frail, but nearly impossible to hit from afar.
Good Bad Bugs: Constantly strafing left and right in tiny increments while running lets you move a lot faster in Hexen II. That's right. Hexen managed to unintentionally incorporate snaking into an FPS.
Defeating Korax may leave one feeling smug, but watch out for the four ghosts that he releases upon death or you might be shredded by them and left staring at Korax's dead carcass with your body dead on the floor. They behave like the Ghosts released from the Wraith Verge, the Cleric's BFG.
Porting Disaster: The PlayStation version. Naturally, you get the port of the same quality as Doom for the Super Nintendo, but with floor/ceiling textures present and made for a console where such quality won't work anymore. Obvious screws include: one-sided enemy/character sprites, choppy framerate along with low resolution, several interior replacements and programming oversights, and, for a dessert, the soundtrack has been butchered in order to fit all those CD-DA tracks into the remaining part of the disc when they could've easily used XA tracks. To make the port even more frustrating, one save eats the entire memory card, compared to Total Meltdown which used, in the worst cases, seven blocks of it! Although, in its defense, it has pretty good FMVs for a game like this and more comfortable controls than the N64 version did. The loading times (from the CD, that means) are not large either.
And, on a side note, that was developed by Probe. Yeah, the same guys who brought the first two Mortal Kombat games onto consoles.
That One Boss: None of the four Horsemen of the Apocalypse in Hexen II are pushovers, but the last one (War) is downright broken. The only thing he does is ride around spamming homing axes. The level you fight him in doesn't really have any places to take shelter and the axes (which do a crapload of damage) seem smart enough to fly around the few corners you can hide behind. Best thing to do is swallow your pride, use an invincibility item and unload all your firepower into the guy at point blank range.
That One Level: One particularly nasty section is a hidden room in the Guardian of Steel level that must be crossed in order to open the way to the secret level. You get teleported into a small room surrounded by several Wendigos (see Demonic Spiders) who must be killed before the walls of the room open to let you out. (or let more Wendigos in) At this point you don't have a great deal of firepower yet, so expect to take a beating.
A good way to deal with the wendigos there is to grab the Wings of Wrath first (near the end of the hub). When teleported in the level, after killing wendigos that trigger the walls to lower, the player can fly as fast as he can for the elevators. The wendigos can then be attacked relatively safely from the main room of the map, through a window, using either flechettes (fighter) or the ranged weapons (cleric or mage). Confirmed to work even on the hardest difficulty.
They Wasted A Perfectly Good Gameplay Mechanic: In the first Hexen, every so often you'll encounter floating platforms, generally represented as glowing sparkle effects and coded as floating "actors" you can stand on. In-game these are used as run-of-the-mill Floating Platforms. Modern source ports for the Doom engine have used these to create bridges and ceilings for proper room-over-room effects, the one major limitation of the 2.5D Doom engine.
Visual Effects of Awesome: The game does some amazing things with the Doom engine, like doors opening outward instead of just sliding up, waves on water, and certain floors collapsing in chunks instead of just sinking down all at once.