The 802.11 wireless modem that Reese and Shaw take from the evidence locker is tagged as having been collected from the residence of Edward Snowden in 2013 and also has an i.d. number of 80211.
"Ice-9" is a reference to Kurt Vonnegut Jr.'s novel "Cat's Cradle". His "Ice-Nine" is a type of water molecule that remains solid at room temperature, which spreads its properties when it comes into contact with regular water.
The simulations the Machine shows to Finch are reminiscent of It's a Wonderful Life (1946). In the film, the main character is convinced he world would be a better place had he not been born. An angel shows him what the world would have been, helping him to realize his life did make a difference in the lives of others.
The car that the Machine drove Finch to the airport while he was in San Jose, CA is a Tesla Model S semi-autonomous vehicle. Tesla developed an autopilot feature that allows the vehicle autonomously drive on roads without the driver ever touching the steering wheel.
As the Analog Interface, Root had a cochlear implant in her right ear. The simulation Root wears a visible earpiece in her left ear.