During one of Adam Warren's Dirty Pair stories, a villain introduces a clone of "good girl" Yuri into the convention the girls are hosting, to shake things up. We first hear about "clone-Yuri's" antics from one of the con-goers (much to real Yuri's distress). Then we cut to Clone Yuri's room and we can clearly see (though the words are never spoken) that she has been literally "screwed, blued, and tattooed".
During a Robin issue during Infinite Crisis, the Teen Titans are in a secret lab looking for a cure for Superboy, after his first beating by Superboy-Prime. Speedy who has HIV asks for everyone to look out for a "Speedy Fix". Notable for making a Black Comedy pun.
Two issues of James Robinson's Firearm involved the title character entering a virtual world based on Glasgow, mostly as a gift to Glaswegian artist Gary Erskine. In one panel, Erskine drew a figure that resembled Alex from A Clockwork Orange outside an underground station. The local nickname for Glasgow's underground railway is "the clockwork orange".
In Watchmen, Rorschach breaks Nite-Owl's lock to get into his apartment. It gets replaced. Then he does it again. It gets replaced. Then the police break in. The lock holds but the door is destroyed. The pun? The lock company was called Gordian Knot Lock Company.
This is less likely to be a pun than an intentional thread in Moore's insanely complicated web of incestuous connections in Watchmen. Ozymandias later refers to Alexander the Great and cutting through the Gordian Knot, which is also, metaphorically, what he himself ends up doing.
Rorschach's foe in prison is short, and his two henchmen are, respectively, nasty and brutish. All three of them perceive Rorschach's comments ("small world", "fat chance", etc.) as being snide remarks about them.... Hrm... possibly true. Must look into later.
Ultimate Spider-Man updates Peter Parker's status quo; he still works for the Daily Bugle in this version, but he helps manage their Internet site instead of taking pictures. That's right, Spider-Man's a webmaster.
The second issue of the Great Ten series is called The Tao of Archery. It involves Celestial Archer, whose real name is Xu Tao.
One of Brian K Vaughan's earlier works was a backup story in a Batman special where, among other things, the Joker breaks into a chemical lab to steal bomb ingredients. While he's there, he decides to amuse himself by re-arranging canisters so the abbreviations on the labels spell out funny things. Boron Argon and Flourine spell BArF, which is "Positively tame" compared to what he did with Copper (Cu) and Niton (Nt).
That must have been a very old canister — "Niton" has been officially named Radon for almost eighty years.
Where do you practice your Deathstroke? In the Deadpool, of course.
In Preacher, two minor villains list their "services" as Sexual Investigators.
In The Wizard of Id, a visitor to the untrustworthy King's castle notices that the King's flag consists of a pair of black X's on a white background. The visitor asks for the name of this emblem. The king moves on to another pun before it mentioned the king is represented by Double Crosses.
Charlie Chaplin did that joke earlier in The Great Dictator, where Adenoid Hynkel's movement is also referred to as the Sons (and Daughters) of the Double Cross. By the way, a different type of double cross (two horizontal bars) has been used in heraldry centuries before the term "to double-cross" was invented (it comes from horse-racing).
ThisMallard Fillmore strip. The punchline sounds almost like a parody of his usual Strawman Political rants; eventually someone figured out it's a Stealth Pun. (Because NASCAR fans are "race-ists".)
A 2009 Housebroken strip had DJ Dog mentioning his plans to expand his empire. His plans include a line of handbags called DJ Doggie Bags, a soft drink called DJ Doggie Dew, and a fashion and lifestyle magazine called DJ Doggie...Fashion Magazine. Maya says she can't think of a better name for the last one without them getting cancelled.
FoxTrot sometimes has the characters making references to Bill O'Reilly or Sean Hannity being on TV — which of course means that the Fox family is watching Fox News.
In the splash panel to thisGarfield strip, Garfield is sleeping on a music staff. The measure he's sleeping on has a rest in it.
A rare unfunny example that's nonetheless good: an arc in The Sandman spin-off The Dreaming was about the loneliness of Matthew the Raven, entitled "The Unkindness of One". (According to Victorian animal-group naming, a flock of ravens is called an unkindness.)
In one issue of Top 10, a bunch of stretchy heroes gawk at a teleporting accident as they drive by. Yes – those Rubber Men are rubbernecking.
Usually, the first words out of an infant's mouth is "Mama" or "Dada/Papa". In Archie Comics, what is the first word of scientific genius Dilton? Pythagoras, the father of Geometry.
Moose, a Literal-Minded individual, provides lots of these. In one story, he was selected as an election candidate. When he appears at the pre-meeting, Mr. Weatherbee asks Moose why he was wearing a track outfit, Moose replies that it's because people are telling him that he's going to "run for office". In another, Dilton's advice to Moose is that he should put his money in the bank to make it grow. Moose decides to grow the money himself, and instead goes home, puts the money in a flowerpot and begins to water it. note If the joke wasn't obvious: he's trying to make a money tree.
In Alan Moore's Cthulhu Mythos/porn comic Neonomicon, wherein there's a literary allusion to the works of H. P. Lovecraft on practically every page, drug dealer/avatar of Nyarlathotep/screaming queen Johnny Carcosa shows up dressed up like Edward Elric. This seems like kind of a random thing to reference, until you remember that one of Lovecraft's short stories was entitled The Alchemist.
Also, the last issue contains the line, in reference to a book of baby names, "A book of new names, not dead ones." This is a pun on the etymology of the Necronomicon (usually translated within the Mythos as "book of dead names") and the title of the series itself.
The waste disposal robot in The Smurfs story "You Don't Smurf Progress" would eat garbage and turn them into bricks that he would expel from his rear hatch. In essence, he was shitting bricks.
Swedish children's comic Bamse has an anthropomorphic wolf named Virginia. Note that you'd have to jump languages to make it work too.