The use of the Patsy ability can be kind of funny, but for the full effect, you need to watch the entire show. First, go into a military base. Find an appropriate target surrounded by people with rifles (anyone with explosives will ruin it). Use Patsy and let the military do the job. They'll go up to inspect the corpse:
Marine: Marines, we did it again!
Using the patsy technique on a soldier who's right next to a demolitions expert is even funnier.
"...And then?" "Well, then he died."
When Alex is instructed to go to a payphone for someone to contact him, he finds that the payphone doesn't work. Taped to the bottom of the phone box, there is a cell phone.
The Prototype comic actually has one, when Alex jumps off a roof, slams into the ground, Hammerfists the pavement so that the Blackwatch troopers and their vehicles are put out of commission... and then steals a cigarette from the mouth of a stunned bystander.
The Web of Intrigue memories have a few moments of hilarity. For example:
Civilian: You can't keep me here! I know my Rights!
Soldier: Maybe, but you obviously don't know much about Martial law.
Then there's this little moment: McMullen believes that he finally has a hold of Mercer's corpse. Working on the computer, he has one screen open to a view from a security camera looking at said corpse. He looks away for a moment, then looks back. Mercer's gone. He stares at the screen, and before the Oh, Crap! expression can quiiiiiite crystallize on his face, Mercer appears behind him and cheerfully (for him) says "Hi, boss." McMullen falls out of his chair in terror.
If you haven't run full pelt down a busy street, snatched an important guy out of a crowd of hundreds, hauled him to the top of a building, absorbed his memories, and then ground-pounded the poor bystanders and/or military personnel wondering what the hell is going on, you haven't played the game yet.
Or even the ridiculous feats that you can do with your superhuman Lovecraftian powers - Literally using another civilian as a surfboard? Destroying a helicopter with a homing flying kick? Destroying a military tank using a Musclemass-enhanced throw of a shopping cart? Running through citizens with your Armor, watching them fly like ragdolls? Yes, you can do those in here!
Radical sending Yahtzee a picture of Cole in lingerie to compete with inFamous (Sucker Punch), who did the same thing with Alex so that Yahtzee would decide which was the better game.
Activate shield power. Plow down busy sidewalk. Watch them flyyyyyyyyyy...
Works with the Armor power, too.
On bloodtox, which is bad for the Infected.
Blackwatch officer: ...In fact, it's so harmless you've been breathing it since you've entered this room. Alex:(in disguise, coughs) Every Blackwatch soldier:(stares at Alex)
If you climb a building by running up it near a marine
Marine: Fucking New York...
The 2010 Christmas gift from Radical Entertainment to the fans. Apparently, Sergeant James Heller has a Nice List and a Naughty List, just like Santa. Unlike Santa, Heller's entire Naughty List consists of the name "Alex Mercer" written over and over and over. AndCole.
A subtle funny moment comes in cutscenes whenever characters are looking at news articles on the internet, for most of the first few scenes one of the biggest stories is the unexplained wave of vandals somehow breaking skyscraper windows, which is in actually caused by Alex running up the sides of buildings.
Any time Mercer is disguised as military and radios command, he won't use the actual voice of the guy he's disguised as. Instead his VA just puts on some ridiculously-cheesy midwestern accent.