The Severed Leg is an easter egg located on top of a building north of Central Park.
The leg is on top of a roof in East Harlem directly north of Central Park on the first building on the right of the road to the right of a ventilation system, it looks like any leg dismembered on Prototype but does not disappear.
The Severed Leg was also featured as a hoax that once you find the leg, you will be sent into a secret level.
Bloodtox is codenamed as Substance A-113A. A113 being an inside joke in animated films created by alumni of CalArts, referring to the classroom number used by graphic design and character animation students at the school that was used by John Lasseter and Brad Bird among others.
Jimmy Fallon DeadEdit
In Prototype 2, during a side quest, Heller has to disguise and follow a Blackwatch patrol. Before the first fight against infected, a Blackwatch soldier named Starnes will comment on how he shot and killed a man that looked just like Jimmy Fallon, a famous television host and actor. One of the troopers will ask for a photo as evidence (which is also a reference to an internet joke "Pics or Didn't Happen") but the leader ends the banter with a, "Shut the fuck up Starnes."
Near a field op in the Red Zone, you might find a Hobo standing on the edge of a rooftop. If you throw something at him, or approach him, he will look at Heller, look back at the edge, then jump off to his swimming pool. In other places in the Red Zone, you may also find civilians doing the same. You can't save them, as they are scripted to die, regardless if you do grab them and set them down safely.
In various places in the city, you might come across an infected citizen that looks similar/uses the same model as the Lady Smith splicer from Bioshock 2. She isn't special in any way, except for appearance.
When engaging the Helicopters carrying the "Heller Detectors", one of the Detector Operators starts spouting gibberish at Red Crown to cover the fact the device is malfunctioning. One of these things he says is he's adjusting the Quantum Entanglements. This is an experimental communications technology in the Mass Effect series of games. Also, there is a Turian Spec Ops regiment called Arbolado in Mass Effect 3.
In Prototype, if you watch carefully the front of any bus, you can see that it has Radical Entertainment's logo instead of having a badge of a car company, or just simply lacking one like all cars in the game.