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: Data bugged enemies get downgraded from boss to standard enemy late in Outbreak. It's not that they're particularly hard to beat (generally, beat them up, Data Drain them, beat them up some more); the problem is that using Data Drain that much repeatedly jacks up your infection rating, and hitting 100% gets you a Non-Standard Game Over. Sure, defeating enemies without Data Drain or waiting long enough can reduce the infection rating. But if you're in the middle of a long dungeon with large numbers of data bug enemies, every fight is a risk for a Game Over.
Ensemble Darkhorse: Mistral was extremely popular, so much so that after she quits in Outbreak, she shows up again near the end of Quarantine for the final battle. Skeith, too, is far more popular than any of the other Phases.
In Mistral's case, part of it was her character, and part of it was that she was one of the previous few magic specialists in the game, with one of the other two being a bit of The Scrappy and the other not joining up until around the end of Mutation.
Skeith even became a playable character in GU.
Fake Longevity: The item collecting quest that unlocks after you beat Corbenik. Fortunately, the game remembers items that you previously picked up, so you don't have to get anything that you previously had.
Faux Symbolism: The relationship between Aura and Morganna in Sign is gone into further depth here, but Corbenik himself is a massive case of this, especially since he gets involved with the former two.
Skeith's original version of it's staff was supposed to be a cross. It was changed into a "Q" to avoid controversy.
Game Breaker: Proper use of the Lucky Shoes becomes this. They grant two spells - one to regenerate your HP, and one to regenerate your SP. In boss fights, this drastically improves your survivability (as you don't need to heal nearly as often) while allowing you to spam your special attacks. Short of One-Hit Kill moves and the possibility of terminal corruption from Data Drain, you become close to unstoppable.
Guide Dang It: There were pools in some levels that could potentially upgrade weapons and armor... or it could downgrade them instead. How could you tell if the pool in question would improve or downgrade a given piece of equipment? Well, if you have memorized a chart where you would compare the apparent time of day from the sky, the precipitation, and the state of the field, you would know. Or just do the general rule of thumb that precipitation meant improving armor and no precipitation meant improving weapons.
Hell Is That Noise: The Net Slum BGM. It has voices in the background of the track speaking in some garbled voices.
The Scrappy: Piroshi, mainly since having him in the party replaces the otherwise awesome BGM with a track of fanfares...
That One Boss: Skeith is ridiculously tough, in part due to being the player's first experience fighting a Phase.
And then after you beat him, you inadvertantly create Cubia.
Macha has an ability that causes everyone in your party to be charmed at the same time. Enjoy helplessly watching your party attack each other.
Tarvos is an incredibly obnoxious boss: constantly switching between Physical and Magical Tolerance like Cubia's Core, casting magic spells that will run roughshod over your party, and possessing an attack that is a guarenteed 9999 damage (a One-Hit KO) to one member of your party, making him a top contender for Skeith's title of worst boss in .hack.