Cinema Snob: You're out of order. They're out of order. This whole system is out of order!
The Critic's announcement to Kevin Baugh of his intentions to invade and how he should just give up is so reminiscent of Wile E. Coyote's similar announcement to Bugs Bunny.
Very likely; Doug Walker is a huge Looney Tunes fan!
In Spoony's commentary, he reveals that Doug describes the Critic as, essentially, a human version of Daffy Duck.
The Critic himself has stated this repeatedly long before that.
Likewise, Film Brain's character seems to be a reference to Chester of the Chester and Spike Looney Tunes.
The Nostalgia Critic phoning everyone to inform them that IT'S TIME seems to reference Palpatine's spiel in Revenge of the Sith. Of course, it then backfires hysterically when everyone calls him back to ask him what he meant... Or to tell him the time.
Spoony going into battle whilst wielding a (rather impressive looking, whilst indoors ) Lightsabre.
Specifically, he was deliberately using the battle stance of Starkiller from The Force Unleashed, but because of how the final shots were edited this was really hard to tell.
Sean Fausz's answering machine message (to the tune of the theme from The Greatest American Hero) is an obvious Shout-Out to George's on Seinfeld. (As a bonus, Critic got Sean's number from Cinema Snob, who also uses the song as his show's theme.)
Linkara also references one of Spoony's Strike Commando reviews when he sees an explosion hit Marzgurl. Turns out she was fine, but it doesn't stop him from telling her about Disneyland and cotton candy.
Linkara, wearing a Power Rangers communicator during the "It's Time" scene, and then going to battle alongside Marzgurl whilst wearing matching colour co-ordinated masks.
He also wears a Starfleet uniform at one point.
Nostalgia Critic's costume, revival & speech about levitation are direct references to the Street Fighter movie, whilst Insano's use & declaration of "Shoryuken" are more a reference to the video games.
Dr. Insano: Whatever happened to the purity of unarmed combat?!
Nostalgia Critic: Well this is just superconductor electromagnetism. Certainly you've heard of it. It levitates bullet trains from Tokyo to Osaka. It will levitate my rocket chair, once it finally arrives. And it also levitates... ME.
Jesus rose from the dead after three days. As did Santa Christ.
The credits are based off of the Bayeux Tapestry, and one of the pictures appears to be based off a famous picture of the Gunpowder plot.
The narrator's final summation is a nonstop Ice-Cream Koan of shout out after shout out, until the Critic shoots him.
The way The Cinema Snob is ambushed in the secret meeting place by the Film Brain shouting with his thick British accent is probably a reference to the movie adaptation of 1984.
Ma-Ti: "Remember your roots, Critic. Remember your roots!"
During Rob's commentary, he notes that Jew Wario deflecting the cannonball back at Baugh was their little ode to Mary Poppins.
In Part 4, when The Cinema Snob asks about who's been listening to Baugh and everyone gets all shifty-eyed, if you listen closely, Linkara is whistling a snippet of his own theme music, as he is known to do. It helps that the theme is catchy, of course.
The final scene with Baugh getting his country back was a shot-by-shot replica of the ending to Home Alone. When the Nostalgia Critic reviewed this movie on the NC Reloaded DVD, he pointed it out as a reference that no one would get.