Apparently there are things called QR-Codes in the game. They're codes on boxes which can be found throughout the game, most of them are in the fist level in that factory. You pull out your cellphone and scan them IRL or whatever and they can be used to take you to a viral website and codes will unlock things like movies on that site. The first part of this IGN movie covers this.
Maybe I am imagining things, but sneaking around in the back allies af Detroit, after you have comepleted the first "mission" and you hear people talking and what not, there can be some intresting things over heard, but one time I noticed that someone, never saw who or where. Was actually whistling the theme for DX:1 that made me giggle.
I wouldn't call the MGS/GiTS references "easter eggs." It's pretty clear that those two series greatly influenced the aesthetic of Human Revolution. I've even seen an interview with one of the Eidos Montreal guys who specifically named them as things the team used as inspiration.
I saw an email on one of the comps from mitnick@schrecknet, a reference to the old Vampire: The Masquerade Bloodlines game. That was a great game and played alot like this one but had a 3rd person mode too.