Carl's T-Shirt has the logo for Science Dog on it, which is a reference to Robert Kirkman's other comic book series, Invincible.
The CDC has been referring to the zombie problem under the code name "Wildfire," and they've been studying it in their secret underground lab. "Wildfire" was also the government's code name for certain categories of pandemic, and the secret underground lab built to combat them, in The Andromeda Strain.
In "Bloodletting," you see for a split second quite a bit of Blue Sky in Merle's drug stash while Daryl is looking for some antibiotics for T-Dog.
As Glenn is explaining his plucky compliance to the group's sometimes insane requests of him to Maggie, he likens it to "playing Portal."
T-Dog compares Daryl to Rambo in his search for Sophia.
In "Prey", while looking for Andrea in the warehouse, the Governor starts dragging his shovel on the ground and whistling a song, much like in The Shining.
In "This Sorrowful Life", when Merle is rounding up walkers to lure towards the governor, the first walker we see, stumbling out of the building, looks a lot like one of the zombies encountered at the airport in Dawn of the Dead.
In "Infected", according to the Word of God, the scene of man getting out bed after turning into a walker and his guts spill out of his body is a homage to a scene from Day of the Dead.
In "Seed", when Carl is picking through the abandoned kitchen, a tin of canned meat can be seen with the brand name "Smeat", most likely in reference to the preferred food of smokers in Waterworld.
The packaging is in fact identical. This is noted to be a common prop, however its prevalence in the aforementioned film - which features a post-apocalyptic setting populated by scavengers surviving on the leftovers of civilization - supports the idea that it may have been used deliberately in this case.
In Episode 2, After finding out the St. Johns are using Mark for dinner, one of the things that Lee can shout at the dinner table is "IT'S PEOPLE!" But this choice causes the group to dismiss you as behaving weird, and everyone, including Clementine, starts eating, so the game even gives you a backhanded slap for trying to be meta.
In Episode 3, a container of Banang can be seen in the cup holder.
The Banang container returns in 400 Days. It's on the pantry shelf in the diner during Shel's story.
In Episode 3, Duck will try to join in your investigation of the missing medicines, calling himself Dick Grayson and you "the greatest detective."