In Episode 8, "Ties That Bind," Monroe holds up the stolen pendant and says "so much fuss for such a little thing". Sound familiar?
In Episode 12, the rebellion holes up in an Abandoned Hospital they refer to as "Echo Base." They are subsequently driven out by a mechanized force with overwhelming firepower led by a man who controls a fundamental force of nature, who is executing the attack to capture another individual who also knows how to control that force, thus completing the analogy to the battle for Hoth in Empire Strikes Back.
This is actually a double shout-out: an abandoned hospital was also used as a temporary base of operations by the resistance in Falling Skies. They, too, were forced to abandon the base after a Curb-Stomp Battle.
Another from Episode 12: Randall mentions that California is under the control of "Governor Affleck," a possible reference to Ben Affleck.
Also Episode 12: Jim Hudson goes by Henry Bemis while working in a library.
Tom Neville's termination from his pre-blackout job as an insurance adjuster qualifies as a shout-out to The Incredibles, when one considers that both Tom and Mr. Incredible (also an insurance adjuster) were sacked for actually trying to help their clients obtain their claims.
In the season 2 premiere, one of the attractions in New Las Vegas is "Meet David Schwimmer, the last surviving member of Friends"
Stephen King Shout-Outs across Season One include: the aforementioned The Stand reference, but also a villain called Randall Flagg... err... Flynn and The Tower. The latter is even referred to as The Dark Tower in the Season 1 Finale.
The wind-up teeth that show up early in season 2 are possibly a shout out to the short story Chattery Teeth.
In Season 2, when Monroe rescues Miles from an ambush, he gives the latter a grin and says "I'm Batman!"