What am I going to do with all this junk inside my trunk?
During my travels, I have picked up many weapons such as LAMs, 12 Gauge Shotguns and Crowbars. These items have clear uses and need no introduction.
Then there are some other items, such as...Soda, Chocolate Bars, and Soy Food? Clearly, these are not the tools of the trade of a hardcore killing machine...or indeed, of anybody at all, and the game offers no explanation for their existence.
Are these items only pickup-able for the sake of atmosphere and to fill those lonely gaps in my inventory, or do they actually serve a purpose?
Even cold hearted killers have to eat sometime! Remember you're a cyborg so there are human parts that need nourishment!
If I remember quickly soy food, chocolate, and soda restore health points. Soda and chocolate are 2 points and soy is worth a whopping 5hp!
You can give food to the homeless boy on the docks just before Castle Clinton to unlock an alternate path into the castle.
Edit: Apparently any food works. Unconfirmed.
Firstly, all items make noise when dropped or thrown. You can use this to distract guards, making them look away from you, or making them run around searching for you (opening locked doors in the process.)
Apart from that, the things you may consider useless include:
Food - candy bars, soy food, soft drinks. These can be given to some NPCs in exchange for information. The boy at the docks in Battery Park is one example. Otherwise, eat them to heal a small number of hit points.
Zyme - give this to junkies or drug dealers to get items or information from them. In modded Deus Ex (i.e. Revision), Zyme also puts you into slow-motion for a short time, so it's actually useful in combat.
Beer - The first time you meet Jock, you can buy him beers to get information from him. Otherwise, drink them to restore a few hit points.
Wine, liquor - no in-game use. Drink them for a small amount of healing.
Flares - set things on fire. Light up dark places, i.e. underwater.
Cigarettes - you can passive-aggressively smoke these in someone's face, to disable NPC's for a short time. They work like pepper spray.
Fire extinguishers - These work like pepper spray too. Also, to extinguish yourself if you are on fire.
The PS20 plasma pistol - an item which genuinely has no use. (Jokes aside: it's a terrible weapon.)