Some more bits of info: When the priest in the Church of Trek says "And Scotty beamed them to the Klingon ship, where they would be no Tribble at all.", it is a reference to the season 2 TOS episode, "The Trouble With Tribbles." Also, "Nazi-Planet-Episode Land (formerly Germany)" refers to a TOS episode where Kirk & Spock visit a planet that's very "Nazi-Land (formerly Germany)"-ish. When Fry takes Nimoy's head from the Head Museum, the head that comes and says, "Yes. Front row!" is the head of Jonathan Frakes, who plays Number One (aka Commander Riker) on Star Trek: The Next Generation.
When Nimoy's head says to Shatner's head, "Bill, you are, and always shall be, my friend" is a reference to Spock's last words (before he dies) in Star Trek II, "I have been, and always shall be, your friend. Live Long and Prosper."
When Fry powers up the Planet Express ship, the buttons make beeps like the ones on the original series Enterprise registry number NCC-1701.
The term "Omega system" is a reference to Star Trek with various systems like the Viridian system or our solar system: the Terran System.
Bender's comment about Melllvar being a cheesy effect is obviously a reference to the cheesy effects in the original Star Trek.
After the first commercial break, during the establishing shot of the ship you hear TOS-ish music.
The sparkly effect of the "TrekFest 3002" appearing is a reference to the cheesy original series transporter effect.
George and Walter sharing a copy of the script may be a reference to their characters, Sulu and Chekov, sharing a "connected" console.
Leela's plan to overload Melllvar is a classic Trek-like plan complete with Trek techno talk.
When Bender is modifying the weapons, or as he put it "'recafoobelling' the energy-motron... or whatever", the "room" he is in is supposed to be like the original series Jeffries Tubes.
When Fry and Melllvar are listing fight-to-the-death episodes, they forgot episode 34, Amok Time, where Kirk and Spock must fight to the death.
The machine gun that Bender finds is a prop from the TOS episode, A Piece of the Action.
Nichelle Nichols' fan dance is from Star Trek V.
The music that plays while the 2 crews are fighting is roughly from almost every hand to hand Star Trek fight.
Melllvar being called for dinner and being referred to as a child is a reference to to the season 1 TOS episode, The Squire of Gothos.
The mention of a self destruct code, Destruct Sequence..., is a reference to the TOS episode, Let That Be Your Last Battlefield, and Stra Trek III.
The music at the end BEFORE the credits is straight from TOS. The music DURING the credits is merely Trek-ISH.
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