I found something small but it was an easter egg that I liked.
Anyone remember the movie Hackers with Angelina Jolie?
Well, the main character was a famous hacker in the movie and he was once known as zer0cool. In one of the emails from a computer you'll hack (I believe it was in Detroit, later in the game) you find an email from something like zer0cool@hacktheplanet.com
Actually the e-mail was from zer0cool@planet.hack, so you were close. Hackers is one of my favorite movies of all time. (Even tho the hacking in that movie was/is nothing at all like real hacking.)
Dade Murphy, aka Crash Override, aka Zero Cool crashed 1507 computers in one day. As a child (11). Something I'm sure mister "Nucl3arsnake" could not have accomplished on his best day as an adult. Anyways, "Hack the Planet" was the name of the show in the movie run by hackers Razor and Blade.
Awesome movie, anyone who hasn't seen it should... *makes a mental note to see if it's out on Blu-Ray yet*
/offtopic/
Dave Mustain IS Megadeth ^^
Founder, leadsinger, lead-guitarist and only all-time member of the band.
/ontopic
Another easteregg is very close to the end.
There is a very white room, where you find
Spoiler:
Building on that, the entire "Sarif" theme that plays when you're in the SI HQ, most notably when you're walking into his office for the first time, is actually a subtle remaking/remix of the UNATCO theme. Link
And the first door code being 0451 just made me laugh like an idiot.