One Hark! A Vagrant strip -  - features a substitute teacher lecturing a class about putting obviously fake names on the register. "'Tits Palmer'? Do you think I'm retarded?" The last panel features the students comforting poor, hurt Tits.
Mike's son in Something*Positive: "Shazam Wil-Wheaton Dowden". According to Mike, "the hyphen is the source of his powers". Mike and the child's mother Tamara had problems with the name — originally it was going to be "Shazam Joss-Whedon Dowden", but Tamara changed it without telling Mike. Mike, who hates Wil Wheaton, was horrified; "I mean, Christ, why not just name my kid 'Hitler-Stalin Pony Raper Dowden'?"
The Santa look-alike whom Jason spent some time visiting in the intensive care ward is actually named "Shirley Koklik". In Jason's words: "I'd pity kill you, but if that name's any indication of how your life has been I want you to be around to show me how much worse it can be."
"Dad, nobody calls me Penny-Jenny anymore, I go by PeeJee." "Bah! Why would I name you Penelope-Jennifer if I wasn't going to call you my little Penny-Jenny?" "Why would you name me Penny-Jenny and then act shocked that I'm prone to violent outbursts?"
Davan's father Fred tries to interest him in the family history by discussing his cousin, a decorated Marine whose name is "Shot", after his alcoholic father's favourite glass.
"He was a hero over in Vietnam." "His name is Shot?" "Saved the lives of four men." "And he never thought to legally change it?" "He did two tours. He might be the most decorated soldier in our family." "Let me get this straight. A man named his child after the shot glass, and no-one thought that was a sign that maybe Child Services ought to be involved?"
A Suicide for Hire client was named "Jeremy Laramie". No, his reasons for seeking death were not connected to his name, sadly. The author's note read "Any resemblance to actual persons living or dead is purely coincidental, but my apologies to anyone named 'Jeremy Laramie'; I'm sorry your parents hate you." Prior to that, there was the reindeer client known by the boys as "Codename Rudolph", whose name actually did turn out to be "Rudy". A potential hazard of being a Talking Animal, one assumes.
Gorgeous Princess Creamy Beamy features Cheesecake Boeing 747 St Cherrywell. The middle name is explained by the fact that her parents are cargo cultists. As for the first name, her mother's name is Pretzel, so presumably it's a family tradition.
Goblins: Life Through Their Eyes has—of course—goblin characters. Many - but not all - of these characters are named by the fortune-teller. One character goes by Hava. His full name? Piss-Off-I-Hava-Headache. There is also Dies-Horribly, Fumbles, and mention is made of one goblin (of the same clan as Hava) who is named Stop-The-Ceremony-I-Swallowed-A-Bug
In Exploitation Now, the character Bimbo's real is Bimbo. To make things worse, she's a sometimes porn actress, and her last name is Moneymaker. Her first name was the result of strong drugs (it was a very difficult labour), and a mother who spoke very little English.
General Protection Fault Software. It's lampshaded by Nick during his job interview in the third strip, and Ki breaks down laughing upon hearing it during a flashback to her own job interview.
Nick: Your company's name is GPF Software, but isn't "GPF" an abbreviation for "General Protection Fault," the most dreaded of Microsoft Windows error messages, from which you can only recover by a complete system shutdown?
Dwayne: Um... I'm not all that creative...
Nick: I personally thought it was a brilliant bit of computer geek humor, sir...
Not to mention the fact that their marketing director, Trudy Trueheart, was born Moonbeam Gertrude Glowerhausen (Hippie parents).
And one of their staff members, Sharon, pointed out that you have to have a sense of humor when growing up in the 80s when your name is S. Murphy.
One of GPF's long-time clients, Goodman Rubber, has a name that's just asking for condom jokes.
Homestuck: Mituna was named for Mithuna, the Sanskrit name for the constellation Gemini. Unfortunately, the name "mithuna" actually means "sexual intercourse" (that's what the Indians thought it represented, rather than a pair of twins).
Although given Mituna's foul mouth and propensity towards sex jokes, it could be considered a rather fitting name.
Being set in England, The Wretched Ones protagonist John Thomas has a very unfortunate full name. His username on an MMO is mynameisalreadyasexjoke.
You'd think Roast Beef from Achewood has an unfortunate name - until you find out that's just a nickname. His birth name was Cassandra.
From Gunnerkrigg Court: "George Parley" is a perfectly ordinary and non-embarrassing name... unless you're a girl. Her parents weren't trying to be cruel; her dad meant to show off his psychic skills by filling out her birth certificate before she was born. He got everything right except her gender.