Jack, also known as "Subject Zero," one of your companions. She is revealed to be a woman, although in very rare cases it can be used as a female given name, and it's revealed in the third game that her real name is Jennifer.
The captain of the quarian starship Qwib-Qwib is rather defensive when questioned on the subject, explaining that ships are bought from different cultures and that it can be difficult to change its registry information.
Due to quarian naming conventions, people who serve on the ships Defrenz or Iktomi carry the name "vas Defrenz" (vas deferens) and "vas Iktomi" (vasectomy). Nice, respectable names, indeed.
One of the mock commercials in You Don't Know Jack: Fifth Dementia is for "The Society for People With Unfortunate Names", including such members as Eileen Dover and her husband Ben.
Also Maggey Byrde who is fittingly named for a Magpie due to her horribly bad luck. When Byrde was six months old, she fell off the ninth floor of an apartment building. Since then, she has experienced a myriad of disasters such as getting hit by various vehicles, getting sick from all sorts of foods and failing almost every test she ever took. And has never once won or even tied at a game of Tic-Tac-Toe. She became known as the "Goddess of Misfortune" as she grew up, and at college, people called her "Lady Luckless". Her current aspiration is to simply "Be an Unlucky Person rather then a Goddess." Like Ms. Oldbag, she's a recurring character.
Another recurring character with this trope is Larry Butz. There's also a saying with that: "When something smells, it's usually the Butz".
For a non-recurring character (so far), we have fat, sweaty otaku Sal Manella, an obvious pun on salmonella.
This one has a strange backstory, though — his original name was "Guy", and the bizarre image editor they used gave him the extension ".brush." After a bit of thinking, they decided to just keep calling him that, but they put out a call for a last name, and someone suggested "Threepwood". Apparently it's a reference to something.
An old DOS game (which had cutscenes animated by the same studio that made some CD-i games featured a eponymous villain named I. M. Meen.
Sniggerbobble, a character from a few series of Mario World hacks as seen in that video. Apart from setting off a few word censors, the name itself is just... incredibly difficult to take seriously. Especially anything else named after it, which added said name in front of a normal word.
EVE Online has the Thukker Tribe. Yes. Really. Some of the system names aren't much better, and even the random alphanumeric 0.0 system names have a few bulkhead bangers.
The actual pronunciation is "Tsao Pee", like the Chinese chicken, but the vocal director for Dynasty Warriors refused to do his research until the Warriors Orochi series premiered in America - six games into the American releases of the franchise for the Chinese warriors.note ...not counting the spinoffs of Empires and Kessen, much less the Xtreme Legends spinoffs either. That raises it to around 10 games! Luckily, the Samurai Warriors crew were comparably unscathed.
In the Phantasy Star series, the name of the Big Bad Dark Force/Darkfalz has been interpreted as Dark Phallus. It doesn't help that, in the fourth game, there's a normal enemy that looks like his sprite in the first game and is called Prophallus.
There's also been reference to the Landgraab/Landgrabb family in nearly every incarnation of the Sims. It's an unfortunate name that also fits, because the Landgraabs are a morally ambiguous rich family. They're a corporate dynasty in the Sims 1 and 2, and greedy aristocrats in The Sims Medieval.
Sims 3 gives us yet another example: Liam O'Dourke ("I am a dork"). His appearance fits his name, and he's a major Base Breaker among players.
Sodom, from Final Fight and Street Fighter. Seemingly, it's named after a city that was destroyed by the wrath of God and eventually gave its name to countless acts of sexual perversion, including homosexuality and even bestiality. But Word of God says he was named after the band.
In Recettear, Tear points out that the eponymous store's name looks a lot like "racketeer".
Aloser Danya in Tactics Ogre. One gets the feeling her parents utterly HATED her. What makes it hilarious is she's one of the deadliest units in the game, being an archer with massive DEX capable of assassinating even fully armored units sniper-style. Just ask Bishop Branta when you see him.
Strangelove, for her love of The Boss, gives an ironically crude codename for the Mammal Pod: The BS-Imago. Although the initials are supposed to be short for The Boss, the initials also resemble a rather crude word (IE: "Bullshit")
Naked Snake's codename was often misinterpreted severely in the sequels to Metal Gear Solid 3: Snake Eater. The "Naked" part of Snake's name was supposed to be a reference to the fact that he does not have any weapons or really anything aside from the clothes on his back. However, the characters think that it stemmed from its most literal meaning (meaning that he was actually given the codename because he wasn't wearing any clothes).
Then there's Major Ivan Raidenovitch Raikov. While "Raidenovitch" may be an unlikely, but possible, Russian patroynmic (where it's the father's name + ovitch for a son) in Japanese Raidenovitch sounds like "Raiden no bitch", or "Thunderbolt's bitch" which ties into his relationship with the local Psycho Electro. In this case it was deliberate, since Raikov is a Take That to Raiden, the protagonist of the previous game.
The Cyborg Ninja Gray Fox was also called Deepthroat (though it's supposed to be a reference to the famous Watergate informant.)
Noob Saibot of Mortal Kombat is an interesting case. His name is the backwards version of the series' co-creators' names, Boon and Tobias. But it's often shortened to Noob, and given the fact that his early appearances has some rather cheap special movies, it fit. The devs seem to realize the joke, giving him a "Troll Hammer" as a weapon in Mortal Kombat Armageddon. In Mortal Kombat 9, his match-beginning quote is "Fear me!" Oh wait, sorry, "ph33r m3!"
Note that this was before the term "noob" was coined, making it retroactively unfortunate.
In the Kingdom Hearts series, Nobodies' names are an anagram of their former self's name, with an x. Xemnas is one such Nobody. His name, unfortunately, also anagrams to "Mansex". There's also Xigbar, which becomes Bigrax, Lexaeus, who becomes E-Sexual, and the mother of all unfortunate names, Xehanort. His name spells, if you remove the X, Rent-a-ho. Or if you leave it there, Rent-xa-ho (Rents-a-ho). Even Marluxia, probably the hardest of them all to re-anagram, at least has one: "U-Miralax" (Miralax is a laxative, by the way).
Night Trap has this with the group called SCAT. (Sega Control Attack Team) You should look in a dictionary to find out why the name qualifies for this trope. S.C.A.T. (Special Cybernetic Attack Team) on the NES has the same problem.
Abobo in Double Dragon, whose name also happens to be slang for abortion.
In Runescape, trolls are names after the first thing they eat. One of the trolls you meet is named "Dad".
The ''Sonic'' series has a six-year-old rabbit called 'Cream'. It's actually Theme Naming with her mother, Vanilla (vanilla cream) and her pet Chao, Cheese (cream cheese), but this doesn't change the fact that the full statement of her name is Cream the Rabbit. And from the classic series, we have "Cucky" the Rooster.
The House of the Dead spinoff game Zombie Revenge has a main character named Stick Breitling. It's like his parents were ashamed of their last name and just figured they would completely humiliate their son.
The game series Myst was frequently target of jokes in Germany, because Myst is spoken like the German word "Mist", which means crap.
In the non-canon Berserk game Sword of the Berserk: Guts' rage, the antagonist is named Balzacnote pronounced like "ballsack".
In Eco Quest: The Search for Cetus, the hermit crab senator is named Superfluous.
The Fire Emblem series actually does have a generic boss named Hyman, who got changed to Reynard in Europe, but not in America. Speaking of bosses, there's also Rommit from Radiant Dawn. And then there are the generic replacements in Shadow Dragon, who have weird enough names already, but lose enough of them and they start getting names like "Lucer", "Auffle", "Laim", "Rejek", "Owend", "Wymp", and "Wieklin"...
Awakening gives us Nah, the half Manakete daughter of Nowi. Her name frequents her no small share of annoyance.
There's a boss in Mega Man X5 known as the Skiver, because he's a Pegasus with sky powers. A skiver is also a term for a lazy person. Mega Man 3 also has a robot master named Hard Man, which they had to have known wouldn't exactly be treated with maturity.
Team Dignitas is a European professional video gaming collective. Dignitas is a Swiss assisted suicide clinic. Michael O'Dell, CEO of the gaming Dignitas, said "We wanted a cool Latin phrase. We didn't recognise the connection until after we'd registered the company. It was a bit awkward."
In Kingdom of Loathing, during the Accordion Thief Nemesis sidequest you end up fighting an assassin known as The Mariachi With No Name. According to his Monster Manuel entry, "The Mariachi with No Name was born Quincy Leslie Droolypants the Third. So ditching the name was a wise choice."
Averted with the Guilty Gear series. After sequels titled Guilty Gear X and Guilty Gear XX, Arc System Works managed to avoid the inevitable outcome by naming the next fighting game in the series Guilty Gear Xrd.
Two Worlds has the evil power known as The Taint. There's also a point where the main character is sent off to talk to a man named Ho note The shortened version of 'whore', and a town called Windbreak note Which sounds a little too close to "Breaking wind".
ProJared: ...which I'm assuming is next to a town named 'Ass'.