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 pretty much 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.
Fridge Brilliance: When paired with a good study of Catholic afterlife, one realize that JC Denton's ending is basically the same as Heaven in the point of view of Catholic, where everyone is joined with Jesus Christ in a perfect democracy and can see Christ everywhere, everyday.
Which also means that all four ending are related to a perception of Christianity.
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.
Electrostatic Discharge on level 3 turns bots and turrests on your side and disables cameras and laser beams, all just by hitting them with a melee weapon once.
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.