Nitpick: The Doctor describes Paris' mutations as being the product of normal human evolution, simply speeded up. However, evolution is the adaptation of the species to one's environment- why would an oxygen breathing species shift to one that breathes nitrogen as part of the evolutionary process when doing so endangers his life within his current habitat on Voyager?
Nitpick: Despite being dead, Paris can be seen gently breathing after The Doctor removes the cortical stimulator from his forehead.
Nitpick: In the final scene in sickbay, Paris says that he and Janeway had "alien offspring". However, they were supposed to have evolved, not changed species. They were always as much Earthly as Chakotay or Kim, just more (d)evolved.
Nitpick: When Tom begins exhibiting the effects of his mutation, a medical team is called for. Throughout the rest of the series, no such medical team appears to exist, to the extent that Tom himself has to pull shifts in sickbay after Kes leaves.
Paris: For a moment, I was everywhere. I mean, everywhere, Captain. With the Kazon, back home with the Klingons, other galaxies, it was all there!
Paris: Maybe we've been looking in the wrong place. What if the nacelles aren't being torn from the ship; what if the ship is being torn from the nacelles?
Kim: The hull of the shuttle is made of tritanium alloy. At the speeds we're talking about, that alloy could depolarize...
Paris: And create a velocity differential! The fuselage would be traveling at a faster rate of speed than the nacelles!
Kim: That means we just have to set up a depolarization matrix around the fuselage!
Paris: That's it! Neelix, you're a genius!
Neelix: I have no idea what they just said.
Kim: In principle, if you were ever to reach warp 10, you'd be traveling at infinite velocity.
Neelix: Infinite velocity, got it. So, that means very fast.
The Doctor: From what I can tell, he's just asleep.
Janeway: Can you wake him?
The Doctor: I don't see why not. WAKE UP, LIEUTENANT!
Kim: We've hit a wall.
Neelix: Well, maybe I can help.
Paris: Great. You know anything about quantum warp theory or multispectral subspace engine design?
Neelix: No, but I'm a quick study.
Paris: Here lies Thomas Eugene Paris. Beloved mutant.
The Doctor: A fitting epitaph, but I don't intend on letting you use it just yet.
Kes: Radiometric emitters are charged and ready.
The Doctor: Begin with 45 rads per second.
Paris: Great... now it'll read 'radioactive mutant.'
Paris: You're losing me, aren't you? I'm going to die.
The Doctor: You're too stubborn to die, Mr. Paris.
The Doctor: It looks like he's having an allergic reaction. What did he ingest?
B'Elanna: Just some of Neelix's coffee.
The Doctor: It's a miracle he's still alive.
The Doctor: You're not going anywhere. At least not for a few hours. I have some tests I'd like to run on Your Majesty before I release you back into the realm of ordinary humans.
Paris: You may proceed.
Paris: I lost my virginity in that room. 17, parents were away for the weekend...
The Doctor: Uh... I'll note that in your medical file.
Brannon Braga cites this episode as the worst Star Trek episode he ever wrote. Kate Mulgrew also said that "Threshold" was the episode of Star Trek: Voyager she was most uncomfortable with, noting that she didn't like the thought of mating with Paris as a lizard.
The changes that Janeway and Paris go through harken back to the Next Generation "Identity Crisis", during which the physiology of Geordi LaForge and a former colleague is altered during an away mission.