It's seems so long before I even touched this sticky...
What about enemy/enemies that are invincible so you'll have to run around and around avoiding it at all costs. Sometimes you can kill it only if you complete a puzzle for it.
Later in the game, after you get your profession preferably, you can go into 'berserk mode' simply by killing enough enemies within the time limit before the gauge is depleted. When you reach the max amount, the bar will drain 1.5X faster then before and killing enemies will only give you 0.5X the amount than before. However you'll be able to do more damage, have higher rate of fire, increase in speed, and all sorts of stuff.
If your PDA is advanced enough, you can hack computers for files and other important stuffs. Depending on your hacking level (I have no idea how this is going to be implemented sadly, use your imagination for this one. Or don't put one at all if that's what you want) you can store personal files and messages from the people that used to be over there. Sometimes you can even view the files in a 'video' mode. The player is not there but you can see whats going on.
What about spray cans that you can shoot on the floor just for fun? A bit useless but then, what the hell.
A railgun might replace the sniper rifle in late game, although it uses fuel (duh) AND sniper bullets. Extremely powerful weapon able to penetrate a long line of the insane army.
Forgot one part, you can go 'inside' your PDA, do whatever you want with it just like a normal PDA (little games to kill your time, calendar, changing backgrounds...). If you're in a wireless connection area you can use your PDA to contact with your lost members. However those members also has to be in a working wireless connection area also. Or you can scrap that idea, just realised you have walky-talkies for that >.>
Being able to interact with almost everything in your environment. Such as breaking vending machines, setting chairs on fire, knocking down trash cans... Whatever. However I think that the Notrium engine was not made to do those kind of things, so unless your extremely skilled (which you already are), don't tackle this into yet until after you finish the game. This has no real purpose into the game whatsoever.
That 'oughta do it. I'm not going to touch this for a long time again so don't expect stuff from me everytime.