Angst? What Angst?: Alex isn't surprised when he/she learns that he/she is the same type of clone as JC Denton, the guy who allegedly caused The Collapse at all. He/she also barely registers distress about the fact that her family was killed in the Chicago attack, though that is mentioned a couple of times. Even when coming face to face with the people responsible, there is no mention of it being a personal tragedy for Alex.
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.
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.
Shadowrun had Chicago being overrun by Insect Spirits as a plot point as far back as 2nd Edition which was released in 1992.
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. A device the size of a test tube, and when activated it sends out a geometrically expanding wave of stuff that spreads across entire city blocks in a matter of seconds. After it is done, everything is left looking like it has turned into ash yet still retaining its former shape. It's one step from a Strange Matter apocalypse.
The Scrappy: The real NG Resonance is this. The holographic one is sociable, friendly and cooperative. The real one is obnoxious and bitchy and, since she's only seen in a single area, has no way of showing any positive traits to her. Many players actually kill her on the spot when they find her because she's just that grating.
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: When the game was first released, while it got overall positive reviews from critics, it received a very mixed reaction from the playerbase. Nowadays, most people concede that as a sequel to the original Deux Ex, it falls flat somewhat, but as an RPG on its own merits, it's actually quite good.
Visual Effects of Awesome: This game came out in 2003, yet in part because of great usage of lighting, the game still looks good over a decade later.