To Star Trek (hence the film's title, the "ship's" name USS Exit Strategy, as well as a scene in the teaser that looks like a couple of the reviewers transporting), as well as the ship-house's dedication plaque: "To Boldly Flee Where No One Has Fled Before"
Mechakara's reaction to learning Terl screwed him over owes a lot to "KHAAAAN!"
Following in Suburban Knights' steps, most of the cast seem to be dressed up as various characters. Unlike Suburban Knights, these are mostly for single scenes or quick gags, but some of them stick for a while.
Ma-Ti continues to play the role of Spock, implanting his "character" into Spoony's body before he died.
Terl's and the Executor's scenes reflect Darth Vader's and the Emperor's conversations. They even lampshade it and get confused which film they're using for reference.
Later, the Executor tries to seduce the Cinema Snob to the "dark side" in a scene reflecting Palpatine's seducing Anakin to the Dark Side in Revenge of the Sith, even doing so in his civilian identity in the same manner as Palpatine.
While it may be unintentional, the garage door on the house strongly resembles the Space Ranger logo.
TheTerminator: A cybernetic killing machine is attacking people that fit a loose description.
Prick's demeanor and opening speech are drawn directly from that consummate Obstructive Bureaucrat, Walter Peck of Ghostbusters. His full name, Lame R. Prick, is an allusion to both Peck and SOPA author Lamar Smith.
The critic getting dreams and a strange pull to be where he truly belongs is straight out of Muppets from Space.
The entire opening sequence of Part 2 is an almost shot-for-shot parody of Ghostbusters, right down to the music used when all hell breaks loose (though the lyrics have been changed from "I believe in magic" to "I believe in science").
When the USS Exit Strategy takes off, CR tells Angry Joe to add 150M to the engines. Joe responds by throwing a mushroom into the engine and a screen lights up reading 150CC.
On Dr. Insano's whiteboard, hidden in the formula is 626 + Lilo.
Terl's line "The Critic will die before these eyes, and he'll know, he'll know that it is I, General Ferdinand von Turrell who encompasses his doom!" is paraphrased from Dune
In fact, that entire monologue, starting with "Oh, I won't tell you who the traitor is, or when he'll attack..." is paraphrased or lifted directly from one of Baron Vladimir Harkonnen's speeches in Lynch's Dune.
More Star Trek references throughout, including Nostalgia Chick being turned into a Borg, Jew Wario reading the Tao Ta Kei (and throwing in the obligatory "Oh myyyyyyyy"), and Paw warning Phelous not to go on the away mission because he's wearing a Red Shirt and Phelous throwing in a Picardesque "Shut up, Wesley!" in response. Seven of Eleven referring to the Nostalgia Chick as a carbon unit may be a reference to The Motion Picture, where a crewmember is converted into a probe for V'Ger.
Jew Wario uses the word "Takei" in place of "gay" at a touching moment between Snob and Luke, which is a reference to Takei's gay rights online spot about the same thing.
JO and CR's shared dreams involving blueprints for some kind of machine is a fairly blatant Explorers reference.
It also serves as a double reference to the Nostalgia Critic as he named Explorers as one of the top 11 most underrated films.
Terl and Zod's conversation has it so that Terl's shots are all Dutch Angles while Zod's are straight. This is obviously a nod to how Battlefield Earth, the film where Terl came from, was shot.
"Seven of Eleven" is a blended reference of Seven of Nine and the convenience store chain 7-Eleven.
At one point CR can see through walls and discovers that 8-Bit Mickey is watching My Little Pony: Friendship Is Magic ("Damn right I am!"). For bonus points, Mickey wears a Derpy Hooves shirt for the rest of the episode.
The Nostalgia Critic thought Sad Panda was a Doctor:
Jew Wario emulates Sulu in the Star Trek episode "The Naked Time" by taking off his shirt and poking Mechakara with a fencing foil.
Of course, more Star Wars references:
The Last Angry Geek's showdown with The Executor is almost taken word-by-word from Mace Windu's confrotation with Palpatine in Star Wars: Revenge of the Sith (as well as the subsequent "I pledge my alliance to you")
The Executor uses the phrase "From a certain point of view..." a phrase used by Obi-Wan to explain why he apparently "lied" to Luke.
The Death Bomb is a obvious allusion to the Death Star.
Allusion to Darth Vader's NOOOOOO and to special editions.
Mechakara's damaged face is reminiscent of the Terminator.
The Executor refers to the Cinema Snob's assistance in killing the Last Angry Geek as "a very successful Tuesday", in reference to the trope named after a quote from Street Fighter.
Lastly, in the final battle, Luke fails to identify what's a Bothan, leading to him confuse the description with other alien species, eventually reaching a Star Trek species in the middle of the conversation.
The ship shooting at the car looks a lot like Eldar Vyper
It turns out that this was accidental, according to the cast commentary. While it is certainly similar, it was changed between the version seen in the trailer (which coincidentally looked a lot like an Eldar Vyper) to a different model (which looks a little less so) seen in the final cut. The reason for this was after realizing the similarity, Channel Awesome wanted to take steps to avoid the Games Workshop lawyers stepping in and having a say about it. That would make this something of an example of Animating Around the Trademarks.
The Critic flying a car in space calls to mind Heavy Metal.
The Syringe that bestows a lifetime of knowledge of the plot into Luke and the lines that follow are directly lifted from Dark City with the name of the syringe itself coming from the film's director, Alex Proyas.
Linkara's Big Damn Hero moment, while being the Sulu/Excelsior of the Undiscovered Country bit, is also very similar to the opening battle of Star Trek: First Contact. Not only does Comicron-1 absolutely dwarf the USS Exit Strategy, heavily pronounced by the entry swoop, but Linkara is even wearing the appropriate Starfleet uniform.
When the Critic prepares to take his first step into the real world, the way he holds his foot out is a reference to the "leap of faith" scene in Indiana Jones and the Last Crusade.
The music and the dialogue from Ma-Ti during the scene where Critic prepares to step into the real world is referencing Joker's words as he thinks the Ships are about to explode in The Dark Knight.
The entire "reality" sequence between the Critic and the writer is a play off the ending scene of The Truman Show, right down to the Nostalgia Critic asking the questions, "Who are you?" and "Who am I?"
The Critic merging with the plothole is a reference to Willard Decker merging with Illia at the end of Star Trek: The Motion Picture.
And it was shot like the Tenth Doctor's regeneration in Doctor Who, just with blue light instead of yellow, and going out with a smile instead of regretting it.
The way the Blue Shell hits the villian's House-ship is very similar to Star Trek VI, when a photon torpedo took out a Klingon vessel. The line "To be or not to be," was also a part of that scene.