During the assault on Deathshead Compound in 1946, Fergus, Wyatt and the rest of the squad are pinned down by heavy fire. And Fergus starts singing My Bonnie Lies Over the Ocean while returning fire and shouting orders.
Fergus: "BRING BACK MY BONNIE TO MEEEEEEEEEEEEEE!"
At the beginning of the game, Wyatt manages to destroy a Panzerhund in the most natural of all possible ways; by having it play fetch with a grenade.
According to the Panzerhund's artist he fought tooth and nail with the animators to make sure the robots acted like 'real' dogs!
A brief snippet from BJ's stay in the asylum has Anya's mother comment that "our daughter has magical powers" for being able to just tell that BJ is alert.
Anya's Father: She's your daughter. I only donated the secret sauce. Anya: Father!
Anya's grandmother tells him any resistance has already been captured and "who knows where they keep them". When he wordlessly turns around to have a discussion with said "who" in their basement, the grandmother turns on the music before he even finishes descending the stairs to hide the incoming noise from said "discussion"
In Fergus's timeline he is moving some boxes around in the Project Whisper helicopter with Tekla nearby doing nothing but writing calculations. The exchange that follows is quite funny, especially when he drops one of said crates on his foot.
Fergus' report back to Caroline when he walks into the Da'at Yichud's cache of technology is one of the crowning moments in the game.
Fergus: Thanks ever so much for the new socks. They're right warm and a snug fit. Yeah, I'm doing well. Although this war has grown a little wearisome. Nothing much of interest ever happens round these parts. Today I landed a helicopter on a nicked Nazi nuclear submarine aircraft carrier. After which I donned a deep-water diving suit, swam down an abyssal trench in the middle of the Atlantic fucking ocean, don't mean to bore you with the details. Long story short, I'm now standing inside a secret vault full of things so magical and abnormal in nature the mind has no recourse but to shudder in bewilderment. 'Course I'm accompanied by a Nazi-killing lunatic and some kind of genius wizard who claims to be on a first-name basis with God Almighty himself. Ah, well, we can only hope for a more stimulating turn of events in the future. Give my love to everyone back home, Fergus out.
While B.J. sneaking around the Nazi checkpoint to try and get the lift open is a very tense and dramatic scene, one bit where you interact with a car has him turning the steering wheel and "honking" the horn, making little driving noises before hitting on an imaginary girl.
B.J.: *Brrr* *Brrr* *Honk honk* Hey, darlin'. How 'bout we go for a spin. *Gets off* Okay. Back to work.
Pretty much any scene that takes advantage of either Vocal Dissonance and/or The Comically Serious tends to get this, such as finding each of Max's toys, getting B.J. to quip in his usual gruff tone.
B.J.: (Picking up a toy telephone) Neat toy. All I had was a pine cone and a box of matches.
When B.J. subdues Keller after he tried to ambush him from his car, the next cutscene has him holding Keller in front of Anya's grandmother so she can slap him in the face. Takes a more serious turn, however, when you realize she's slapping him and screaming at him because he is responsible for the murders of her son and daughter-in-law.
When B.J. gets the Laserkraftwerk, you can practically hear the gears turning in his head as he holds the LKW in his right hand and the Laser Cutter in his left hand, then he simply tosses the Laser Cutter away in favor of the newer BFG.
When you came back the resistance greets you like nothing happened.
The Fetch Quest gets more ridiculous as you go find a welding torch dropped into water. The game sics Supersoldatens on you.
B.J.: "Long walk for a lousy welder."
After spending a lot of time proceeding through and completing one of these Fetch Quests, Set then bluntly orders B.J. to deliver a note to Anya... who is sitting mere steps away from him. At which point, B.J. is clearly starting to get a bit sick of all this "fetch this and deliver that" shit:
B.J.: [Grumbling to himself] Like I'm the goddamned errand boy...
The journal is a touch sour about the latest Fetch Quest too.
Throughout the game, B.J. can find various vinyl albums, which contain popular pop songs of the era. These are songs from the real world, but covered by artists of the new regime. The one that takes the cake is probably the game's cover of the Animals' "House of the Rising Sun", replacing the original instruments with tubas and accordions, turning it into some sort of strange German folk song.
"Mond, Mond, Ja, Ja", supposedly by The Beatles, isn't as inherently funny on its own when you first find the record playing it. What makes it hilarious is when it actually plays in gameplay, while you're actually on the moon. And getting shot at by a giant robot while calmly riding a tram between sections of a base on the moon.
Being on the moon, looking in the cabins, seeing a computer, what is it playing? Wolfenstein3D The letter found on the moon base is also quite funny - it's a personal ad that plays up the career of a Space Marine searching for a woman with "child-bearing hips" for 5, 6, perhaps 12 children.
A more subtle moment, but during the montage that accompanies B.J.'s "concrete for miles" speech, the Nazi prison guards driving the paddy wagon look like they're bobbing their heads to the rockin' background music.
BJ drowning a Nazi in his own piss is funny enough on its' own, since science has proven that you cannot be too violent to a Nazi. However, it becomes even funnier if you watched Yahtzee's review of the game before buying and playing it. During the review, he uses the drowning-a-Nazi-in-his-own-piss thing for an example of the aforementioned 'cannot be too violent to a Nazi' theorem, but he never indicates it's actually something that happens in-game, leaving players who saw the review first and played it second to realize that he wasn't taking the piss. The sheer fact you flush the toilet as well meaning you are committing death by swirlie. As well as that, when drowning the Nazi in his own piss doesn't go as quickly as BJ would like, he immediately falls back on his standard takedown action, and stabs him in the back of the skull.
When going after the Nazi scientist in the train BJ has a truly spectacular one-liner to give:
B.J.: "I'm comin' for you, you Nazi fuckin' space man."
Also during the bridge level, if you fall off the bridge, BJ will have just enough time to lament it before he hits the water.
B.J.: "... stupid way to die."
At the end of the "pure blood" test on the train, the Frau reveals that it's all nonsense, just some photos she took. Then she says she can spot impure blood just by looking at someone, which is funny if you know that BJ is a Polish-American of Jewish matrilineal descent.
First one: "Well, that seems to be in working order."
Second one: "This is becoming some kinda compulsive behaviour..."
Frau Engel hopelessly attempting to stop a hijacked Mecha by hitting it with a riding crop.
In the prologue after taking out a machine gun nest:
Fergus: "Alright, listen up, people! Captain Blazkowicz has seen fit to clear us a path! We are moving out, and you will show him the courtesy of not getting yourself neither shot or killed by the stomper! Understood?"
After B.J. steals a supply train from the Berlin catacombs, Wyatt is his usual chipper self when they meet up:
Wyatt: Right on time, Captain! Walk in the park, was it?
Wyatt: ...Okay. Well, I'll just get to work.
When storming the London Nautica the first time, while sneaking through the elevator shafts you come across a stalled elevator with two officers trapped inside. One of them is clearly getting a bit nervous about being stuck in an elevator during what has obviously been a bit of a disaster. The other snaps that it's perfectly safe, there are four emergency brakes and all of them would have to fail for the elevator to crash. Good thing for them there isn't a half-crazed Nazi killer lurking on top of the elevator who needs it to plummet to the bottom in order to ride the counterweight he's standing on right to the top and now knows to shoot the emergency brakes... oh. After shooting the first brake, B.J. will muse on What Could Possibly Go Wrong? and will say point-blank he should stand on the counterweight. Which has bright yellow footprints painted on the top for no discernible reason. One has to wonder how many playtesters bungled this setpiece to warrant that much signposting.
In the middle of the Eisenwald Prison escape, if the player takes a side hallway while Fergus continues to fire down the main corridor:
Fergus: Where the bloody hell are you going, Blazko? Oh - you're flanking them! Carry on!
After dropping the Spindly Torque on the Gibraltar Bridge, B.J. and Wyatt (or, alternatively, Fergus) have this exchange: