Seven and the Doctor placing the entire crew in a stasis sleep in "One".
Now it's just our hero and her plucky hologram sidekick. (blares Red Dwarf theme)
On that note, Chuck notes the two colliding planets in "Ship in a Bottle" and muses that Lister's playing pool again.
Why does episode "Evolution" begin with Wesley passed out in a lab? He has been up all night making crystal meth, because he's found out that he has an inoperable lung cancer and has turned to life of crime. Wesley is breaking bad!
"Yelling at Kaylee? That's like punching Fluttershy, it's just plain wrong."
Referring to the unicorn in Decker's dreams in Blade Runner as Rarity.
While mention fanfic in The Legend of Korra review he says he's heard there is a really good crossover one being written. 50 Shades of My Little Pony.
During the "Yesteryear" review when discussing kids cartoon dealing with the death of a beloved animal.
SF Debris: It's like the time Rainbow Dash broke her leg and had to be put down. Rainbow Dash: I can still fly! *BLAM*
From the Game of Thrones pilot: "By the way, 'Screw you and the horse you rode in on' is only a figure of speech. Don't expect her to literally screw the horse! Though this might have inspired the Game Of Thrones/My Little Pony Slash Fic I'm sure somebody has written somewhere."
In "In The Flesh," Janeway demands that Seven continue to make bigger and deadlier bombs to use against Species 8472. After she demands more of something called "the Galaxy Eater," Seven says that they're out of nano probes.
Even when beamed over to another ship which is hijacked by Romulans, Picardo has a moral imperative to treat them. "When you call yourself the Doctor, it's like a promise you make!" ("Message in a Bottle")
In AvatarTheLastAirbender: Fire, he notes that Team Avatar needs a bender. Smash cut to Bender singing Karma Chameleon. When he corrects him self, saying that the need a fire bender, there's another cut to Bender belching fire.
Another shows up in the OVEG to Counterpoint, Janeway paraphrases Bender:
Janeway: This is the worst kind of treachery: The kind against me.
The Farscape episode "Out Of Their Minds," has multiple references to Futurama, partially because they had also done a similar body-swapping episode (made many years later, but still).
At the end of the Andromeda episode "Dissonant Interval," which was penned as a possible series finale, Dylan goes to meet his destiny...and meets himself. Chuck wonders if this would make Patrick McGoohan facepalm.
In "Wormhole X-Treme!", Marty tells O'Neil that the stuck-up producer's last show was about a dog that solves crimes. Chuck then says that Poochinski was a real show; they had a pilot made, anyway.
There is a scene in "Booby Trap" where Riker talks about the trap that's draining the shields and exposing the crew to deadly radation. Chuck!Riker finishes with "The only solution is to give into despair and transform into witches."
Kyubey's Google-search on ways to prevent the heat death of the universe turns up a Schoolhouse Rock reference/pun "Loli, loli, loli, get your adverbs here!"
Review of The X-Files pilot episode mentions that a local medical examiner at the Adventure Town is uncomfortable when agents have a grave exhumed. He's either hiding something or they hired The Benny Hill Grave-digger and Gardening Services Company. The latter is likely as the coffin is dropped and rolls down a hill.
His Hogfather review includes several quotes from other Discworld books.
Occasionally, in Star Trek reviews, a given piece of technobabble either works or fails to work "because quantum", the favourite dismissal by the wizards of Unseen University when something magical, technological or both fails to work properly for reasons they don't or haven't even tried to understand.
In "Datalore", he first describes the Crystalline Entity as a 'Lovecraftian horror that eats planets', then when Lore reveals he betrayed the colony to it, asks if he got the ability to fly through space on a surfboard as a reward.
In his KOTOR Let's Play, he references 20,000 Leagues Under the Sea when mentioning that a Jedi named Nemo would be perfect for an underwater mission involving a submarine.
Edith Keeler was supposed to die in a traffic accident, but instead would go on to work with FDR to keep America out of the war too long, so that the Axis powers won World War II thanks to the retrieval of the Ark of the Covenant.
Compared Janeway's self-assimilation to the Shaun of the Dead's "walk like a zombie" tactic.
Chuck's explanation of World War II (seen on its own in the CMOA page) has about ten Shout Outs per second, even if he can't remember what that U-Boat was up to.
In Part 1 of "The Killing Game," Chuck describes the situation the Germans were facing: the Soviets were approaching from the East, the Allies were coming from the West, Rome was taken, Hitler was angrily throwing pencils at maps...
"Parallels" (of TNG): Worf's goodbye to Troi before returning to his reality has a spoof of the final speech from Casablanca:
Worf: It doesn't take much to see the problems of a strapping Klingon and a Human/Betazoid mongrel don't amount to a hill of beans in this crazy galaxy. But if that shuttle gets off the ground and I'm not on it, I'll regret it. Maybe not today, maybe not tomorrow, but when I meet your mother, my God will I regret it.
To Mass Effect 3 when he notes what if Kirk used the Guardian to go back and change things? Cut to it happening the exact same way, but in a different colour. Also doubles as a Stealth Insult to the infamous endings of the game.
Mass Effect earns another reference in "Terra Nova", with a crack that the asteroid impact on that planet was clearly the fault of the batarians - an asteroid-based attack on a colony named Terra Nova, by batarian terrorists, was the plot of the first game's Bring Down the Sky DLC, which is integrated into the PC release.
Earlier in the "Terra Nova" review, he stated that the obvious culprit for who attacked Earth's first long-range deep-space colony was the geth, because that's the sort of thing they do.
Paradise gives a fairly vicious Take That to the endings, referring to how frustrating it was. "Why don't you just make the ending red, blue, and green if you were just going to make it fucking infuriating?!?"
The attack on the Salarian colony in "Ensign Ro" clearly was done by the krogan, though the only people who'd would get that joke are busy today.note (the episode in question was released the day Mass Effect 3 was released.)