Dr. Horrible is full of this: On his blog, the Doctor mentions transporting several gold bars from a safe. He lifts up a bag of brownish "cumin-smelling" liquid and says that the molecules shifted in the transportation Bouillon/gold bullion
Also, in the song "Neil's Turn" on the Commentary, Neil Patrick Harris is stuck alone and in the dark in the studio, and sings, "What's with all these weird cords?" just as the music plays a bunch of "weird chords"
Fools Gold: There is a mention of a Giant Panda who drives a truck containing stolen ingots of lanthanide metals. His truck is #71 and his name is Lu. 71 is the atomic number of the lanthanide Lutetium. Its symbol in the periodic table is Lu. Lu is also a common Chinese surname.
PZ Myers is a biologist with a love for octopus and similar creatures. When Paul, the psychic sports predicting octopus died, he went back and forth describing his feelings on the matter, using the phrase 'on the other hand' seven times.
This blog post is written by an author who enjoys puns based on the origins of words. "None of the little particles in the universe had gotten the idea that one might turn yet." "Universe" comes from Latin roots uni and vertere—"one" and "turn".
In one episode of Sassy Gay Friend, the title character makes his entrance out of a closet.
Einstein VS Hawking: "I'll "school" you anywhere—MIT to Oxford"
"… when you try to put your little p-brane against this kind of mind …"
Mario Bros VS Wright Bros: "Sorry, Wright Brothers, this time you chose wrong."
"You might fly like a hawk, but you fight like a kitty."
Seuss VS Shakespeare: " Oh, no, we'll smash your globe."
"You gettin' upstaged Bill. Yo you just got played" is especially stealthy.
Elvis VS Michael Jackson: "I've seen every record you set, man I beat it."
Gates VS Jobs: Steve Jobs saying "I got a PC, but it wasn't from you," to Bill Gates. One of the stealthiest ones yet.
He also says he'll "bring up some basic shit".
Later, HAL 9000 offers "I think different from the engine of the days of old", referencing both the former Apple Macintosh slogan and Charles Babbage's difference engine, the first computer.
"You blow, Jobs" (complete with hand motion)
Obama VS Romney: "You're all Barack and no bite."
Bieber VS Beethoven: "You wanna trade blows? You can't even hit puberty!"
Cleopatra VS Marilyn Monroe: "Gettin' 'Lo on Marc Antony."
Freddie Mercury VS Frank Sinatra: "You're the least talented rat in your whole pack of rodents!"
Doc Brown VS The Doctor: "Now Dalek my balls!"
Bruce Lee VS Clint Eastwood: "Kung F-U!"
Batman VS Sherlock Holmes: "You're a batshit crazy basket case!"
"Dissing these dynamic douchebags…"
Martin Luther King VS Gandhi: "Flatten your style like bread, Naan violence!"
"You would know about bread, Dr. Birming-ham sandwich."
"With protests and women, the same advice goes/ Always stay away from the ho's (hose)."
"I fought the caste system, but you still cannot touch this!"
"I'm the King of civil rights"
Hitler VS Vader rematch: "I strike back hard against a Nazi!"
Mozart VS Skrillex: "You died baroque and worthless"
Rasputin VS Stalin: "The last man who attacked me lived a half-life!"
A good one concerning Rooster Teeth is the company name itself and it involves a vulgar insult used in Red vs. Blue. That insult? "cockbite".
Late in Volume Two of RWBY (also made by Rooster Teeth), though it's not delivered like a pun and nobody reacts to it like one makes it easy to overlook...until you realize where they are.
Yang: I guess this is what we trained for.
Typical viewers of video game streams are affectionately known as stream monsters. Twitch.tv's most popular chat face is called "Kappa," as in a literal stream monster.
Noob has a possibly accidental one that can be found via Bilingual Bonus. Gaea has two reccurring (in-series) nicknames: one is "Dame Gaea" in the original French, which translates into "Lady Gaea" in English, the other is "Gaga". When these two come together...