Lampshaded in "Barge of the Dead" when Torres casually wrecks one to save herself time, like Mario sacrificing Yoshi into a pit for a sake of a double-jump. This earned her a trip to the Principal's Office:
Janeway: Those things are irreplaceable, you know.. ..HAAAAHAHAHAHAHA! Go give it a Viking funeral and then replicate me another one— with leather seats and a cigarette holder this time.
"Ancient Chinese Secret, Huh?" for whenever they refer to something in Earth's history as "Ancient," regardless of what time period it took place in.
"Lazarus of the Week" for when a crewman, well, pulls a Lazarus.
Tom Paris gets a "Jesus of the Week" for actually managing to raise himself from the dead. Note that this happened without Alien intervention, advanced technology, or Time Travel being involved. He was dead one minute, then alive the next all by his own doing (okay, there was genetic mutation involved, but since it was simply his body's own biology that resurrected him it still counts), hence this exception.
Ilia got a "Damn Dirty Mutant Lazarus of the Week" in Star Trek: The Motion Picture for dying, being brought back as a bastardization of science, and then dying again (maybe).
And, of course, "Stupid Neelix Moment" (in pretty much every review involving Voyager's resident Alien Scrappy). Also that Neelix is a shithead. invoked
As a companion gag, he gives a plus one bonus to his "Final Score" for any Voyager episode not featuring Neelix in the episode at all.
Caption: No Neelix. Life is good.
"Shattered" still netted a Stupid Neelix Moment, though, as the episode opened with Chakotay squirreling booze away from the lice-covered stalag upstairs.
He avoided giving the episode "The Void" a Stupid Neelix Moment, although at the end of his video, Chuck inserted a clip of Neelix, and while not a Stupid Neelix Moment, it did cause Chuck to Hulk out.
In a bit of a shocker (or a sign of the Apocalypse), he actually gave the episode "The Disease" (where Harry Kim catches an alien STD) a bonus point for featuring a Neelix moment which advanced the plot in a helpful, non-annoying manner. To paraphrase Chuck, "it was as if Harry had used up the supply of shame in this episode."
In "Tsunkatse" he does not award a Stupid Neelix Moment despite the fact that Neelix appeared in the episode, because he had been spending his time earlier that week watching Battlefield Earth and thus couldn't find it in him.
Since none of the other Trek shows feature a regular character as consistently annoying as Neelix, he resorts to "Annoying Character", for the person who's the most annoying in the episode.
Amazingly, Wesley Crusher, who is an actual in-universe Creator's Pet, has only got this award twice so far. On top of that, Wesley's every single scene in "Menage a Troi" is welcomed as distraction from stupid plot. Much like "The Disease", the usually annoying character suddenly being competent is only redeeming part of episode.
Captain Okona has received this award in two TNG episodes, despite only appearing in one of them ("The Outrageous Okona", the other one being "The Game"). That's what they get for keeping Okona in-canon.
'...because Chakotay has always been into (sound of dice rolling) [Insert Interest here]' Examples include 'Paleontology!', 'a fervent... Anthropologist!' and 'a keen interest in... Boxing!'
Harry got his own variant in "Bride of Chaotica" when he voiced annoyance at the lack of Captain Proton slave girls as advertised. Because he's always been into... (roll roll roll) 'Heterosexuality!'.
The "Off Button Hypospray" used when Instant Sedation is called for (or even uncalled for), and "the Medical Phaser" for when the OBH isn't sufficient or fatal enough for some hapless soul.
In his Season One TNG reviews, he jokes that Picard keeps firing his chief engineers at the end of the episode since we rarely saw the same one twice until they settled on Geordi.
Alluding to Seven and Chakotay's Last Minute Hookup in "Endgame" by noting sarcastically that she clearly wants to hump his brains out some day.
Variations on, "And once again our "survival expert" nearly gets everyone killed!"
The TOS movies frequently re-use stock clips from the previous film as 'surveillance' footage. Chuck prefers to think Starfleet are firing up their brand-new Trek Blu-Rays.
Star Wars allusions in First Contact. Hey, The Force makes as much sense as Picard's sudden Borg telepathy.
"I sense something. As if a bit part cried out in terror and was suddenly silenced.''
Confabs between Captain Sisko and his franchise counterparts. Picard gives technobabble solutions, Kirk suggests giving a Kirk Summation followed by hitting someone, Janeway is her typical dastardly self, and Archer is gibbering in a corner.
Inverted in "In a Mirror, Darkly": Archer's in charge, with Kirk, Picard, and Sisko all sporting Beards of Evil. In this universe, Janeway (also bearded) is a harmless Granola Girl.
Jake Sisko and Chris Pine's Kirk get in on one of these in the review of "The Visitor". Pine's Kirk gets swiftly beaten up by Shatner's Kirk.
In his X-Files reviews, referencing stereotypes about the US state an episode is set in—such as Idaho and potatoes ("Deep Throat") or Wisconsin and cheese ("Fallen Angel").
Fan Nicknameinvoked: Many jokes involve alternate names for things, combining personal opinion, behind-the-scenes facts, Actor Allusion, and more.
Captain Archer is frequently called "Duchess," to show how insane he is.
Klingon "Bird Of Prey" warships (specifically the one in Star Trek IV: The Voyage Home) the name "Kia of Prey," because compared to the Enterprise, they look about as primitive as a Kia (a type of car).
Janeway's sanity inspired the nickname "Captain Crunch."
He couldn't remember the name of the friendly Peacekeeper female from one episode, so he calls her by the very apt title of the episode she appeared first in: "PK Tech Girl." (Peace Keeper Technician)
He nicknamed one of the Andorians from "The Andorian Incident," "Andorian Colin Mochrie" after his strong resemblance.
Janeway apparently really likes Mexican Food, claiming in one instance that "She needs to kill off Maquis more often" because of the nachos they serve at their funerals, and in the review of "Ashes to Ashes," she claims that the only reason that she attended the funeral of (a different) deceased crewman was because they served tacos.
"Poor, dumb Harry." Mostly towards Harry Kim, but also to Harry Sullivan on one occasion. Sometimes, he uses the basics of it for other characters, like John Crichton or Bernie Wiseman.
It's not a joke unique to Chuck, but he uses the following enough for it to be a personal trope of his: following up a sentence with some structural ambiguity with, "... the (x), I mean, not the (y)."
"The shuttle comes back with Harry Kim on board looking badly dehydrated. Harry, that is, not the shuttle. "
When something horrible is going to happen to the crew of Voyager or the NX-01, it's "too good for them, I say!" This is more infrequent now, perhaps for the same reasoning he doesn't preface Enterprise or Voyager episodes with the old "Welcome to the idiocy" line: namely, it made it seem like he was just complaining about those shows instead of trying to provide a balanced review.
"Romulan marijuana" is the drug of choice in the Star Trek universe, apparently, whether Picard is tripping on it or Janeway shooting down an enemy ship to protect her stash.
Torres will always and forever be the Chief Engineer "who couldn't identify sh!t with a tricorder".
Later corrected to "... even with a tricorder!"
An increasingly common one is an alternative to Good Angel, Bad Angel: Shoulder Spider, who advises those on whose shoulder he sits to eat other people... and occasionally all of creation. First showed up in "Year of Hell," for Janeway, again in a far more sophisticated fashion in "Remember Me," and most recently in "Scientific Method," again appearing to Janeway.
In his Stargate SG-1 reviews, the very first time Lord Yu came up Chuck immediately seized on the Who's on First? joke that even the show itself eventually decided had overstayed its welcome, and ran it right into the ground. We'll see if he keeps using it.