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.
Cult Classic: Crack Dot Com went under a while after the game's release, but it's still a well-regarded game even today, and its mouse-aim style of control is also emulated in other PC 2D shooters.
Demonic Spiders: Some of the tougher varieties of mutants definitely count.
A flyer with the Napalm weapon basically means flying instant death.
Fridge Logic: The game's Excuse Plot doesn't even begin to explain some of the weirder level design choices. Why does a maximum security prison need giant underground caves and lakes? Where's all this green alien coral coming from? Why is a maximum security prison full of spacious wide-open areas that anyone could easily escape from if they just jumped into the background? All of these made more sense with the original "lone agent infiltrating an alien base" plot, but with the change in plot it's now just confusing.
Paranoia Fuel: Mutants can pop out from anywhere, at any time. The loud roaring noise they make when they finally do is pretty startling as well.
Arguably worse is when you see their cocoons in plain sight. Now you're just waiting for them to attack, but you still don't know when.
That One Level: Anytime you have to outrun the "Big Bomb" hazard as the developers made these scenarios to allow no room for mistakes. The worst is when you first encounter it, you have to fight hoards of mutants and you barely have enough time to even get out.