Archie Comics: Something like "I'm Mr. Chovy, and I want to know why my daughter Ann didn't make it into the yearbook."
The Archie comics continuity saddled poor Sonic the Hedgehog with the name Olgilvie Maurice Takeshi Hedgehog when under the pen of Ken Penders. Ian Flynn, however, set it up so that Sonic got his name legally changed to "Sonic".
The Crush!Yiff!Destroy! review of Extinctioners said it best: "Each character is also burdened with a ridiculous name — look, there's a gorilla named Warfare! And a panda named Pandamonium! And a phoenix named Phenix!"
Marvel Comics' Nova. His name is Richard. Richard Ryder. Now what do people call Richard for short?
Also, DC villain Blackguard, real name Richard Hertz, prefers people to call him Dick. He doesn't see what's so funny about it.
The eponymous character of The Adventures of Tintin can be considered this in certain parts of the Philippines. Specifically the parts where the local language's (the Philippines has several) colloquial term for, well, the penis sounds exactly like Tintin's name.
Young Miracleman's real name was Dickie Dauntless. This was lampshaded during the Alan Moore run when Miracleman's wife Liz expressed her disbelief that someone with such a name ever actually existed.
It's been pointed out several times in-universe that John Stewart, the African American Green Lantern, shares his name with comedian Jon Stewart. It's treated as a humorous thing, such as Arsenal asking if Kyle Rayner really knows the host of The Daily Show after he mentions John's name.
Speedball from the New Warriors shares his name with a mixture of cocaine and heroin. Made even funnier when the New Warriors teamed up with Captain America for an anti-drug special.
His teammate Night Thraser was a Fad Super made to cash in on the popularity of skateboarding in the early 90's. Several characters (such as Spider-Man) have commented that outside it's initial context, "Night Thrasher" sounds kinda nasty. Such as this little gem from Civil War:
Coldheart: I'm not getting taken down by Goldfish-Girl and the Bondage Queen!
Namorita: Beg to differ, Coldheart.
Night Thrasher: Could we cut out the part where she called me "The Bondage Queen?"
Microbe: Oh, yeah. Because "Night Thrasher" sounds so much straighter.
Lemar Hoskins, the thirdBucky and the first African-American to use the name. When it was pointed out to him that "Buck" was a derogatory term for a black man, Lemar changed his name to Battlestar and never looked back.
Which makes it even odder that there was another black Bucky. A Young Avengers one-shot had Steve Bradley, the child of Patriot and the female Falcon, as the new Bucky. Apparently neither parent was aware of the incident with Lemar.
Young Avengers member Asgardian (who didn't even have anything to do with the Norse pantheon) was advised by his teammates to change his hero-name almost immediately after he went public with his relationship with male teammate Hulkling.
There's a Decepticon named Overload. Which is alright, until you remember it's fanon slang for a Cybertronian orgasm...
The Hungarian translator of the Marvel The Transformers comics changed Breakdown's name to Vibrator. Even hardcore G1 fans agree that this is one name change that's best forgotten.
There's a mildly obscure Transformer named Nexus Maximus, which sounds fine, until you realize it's also the name of a brand of sex toy. Hasbro changed the official name to Nexus Prime.
There's no way to not imagine horrible, horrible things when presented with a character named Drillnuts (he turns into a boll weevil, you see). Summed up succinctly by the TF Wiki itself:
"OW OW OW OW OW OW OW OW OW."
Despite actually having the title first, Marvel briefly changed the Black Panther's name to "The Panther" and later "Black Leopard" in order to avoid comparisons with the black radical group of the same name.
This was lampshaded in the crapsackAlternate Universe story "Ruins," where T'Challa was an actual member of the Black Panther party.
Teen Titans had a fire-element character named Joto, which suitably means "heat" in Swahili. However, when adapting the character to the cartoon, writers were horrified to learn that the far more familiar, Spanish translation of the exact same word is "faggot." He was renamed Hotspot and remains so, even in the comic.
In recent portrayals of his origin, the child who would become Superboy of Earth-Prime (which was supposed to be the real world) was picked on by his peers for being named Clark Kent, "after a comic book character."
In certain parts of the world the name Peter has been given the same treatment as Dick; so it may come as a surprise to the people in those places that no one has yet asked, "So... where DO you Park your Peter?" (And then there's this certain Alien Symbiote obsessed to become the answer to that question...)
Sir Peter Parker is a former head of British Rail.
Poor Dick Grayson. Luckily for him, he has a great sense of humor, so he makes a joke out of it. "I'm Dick." "What?!" "No, no, that's my name." Cue smarmy grin.
Starfire: I love Dick!
Beast Boy: So I've heard.
In MAD Magazine, Ziegleveit B. Schtoonk was an Al Jaffe character who recurred in his 'Snappy Comebacks to Stupid Questions' series. The stupid questions would invariably be about his name, but what do you expect if you engrave something like that on your nameplate?