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: Armored Templars if you are going for a Pacifist Run. They can't be knocked out (Doing so will cause them to explode, killing both you and the Templar), are immune to flashbombs, gas grenades, and boltcaster darts, usually have powerful weapons like rocket launchers, and come in large groups. Cloak is necessary to get past these guys if you are going for a no-kill run.
Disappointing Last Level: There is a certain point where all the plot threads have come together, after which the level design in the remaining couple of levels in the game becomes much less... "immersive", shall we say.
Game Breaker: The Spy Drone Biomod, at the highest level, can knock guards unconscious. Combine this with a repair bot, which constantly replenishes your bio-energy, and the Cloak biomod, to make you invisible, and you can secure an entire map from the safety of one room. This is a complete about-face compared to the nigh-uselessness of Spy Drone in the original Deus Ex.
Electrostatic Discharge on level 3 turns bots and turrets on your side and disables cameras and laser beams, all just by hitting them with a melee weapon once.
Hilarious in Hindsight: The game has Chicago destroyed in a nano-terrorist attack by a member of a fanatical cult in the intro and Seattle is featured as one of the levels in the first half of the game. Cue another Cyber Punk game released exactly a decade later featuring Seattle as its main setting and Chicago being ravaged by an insectoid invasion channeled out of human hosts from a dark occult-like ritual perpetrated by a seemingly innocuous Happyology-like organization.
Ho Yay: The Seattle Minister of Culture invites some kind of artist to his apartment, and asks you to be his chamber boy in hopes that you will make it a threesome. This is quest-relevant but not explicit.
Nightmare Fuel: The Grey Goo bomb is truly frightening. It's one step from a Strange Matter apocalypse.
They Wasted a Perfectly Good Plot: While many praised the idea of having no side truly be evil (except the Templars) and the idea of playing for multiple factions, the execution on the other hand....
Vindicated by History: Mildly; the game was savaged by critics and players alike at release. Years later, it's looked on a little more favorably by most, in the "not a bad game, but a bad sequel to Deus Ex" sense. So Okay, It's Average is an improvement over the original reception.