In Death Note, Mello joined the mafia after leaving Wammy's House.
Baccano! takes place during the American prohibition era. It prominently featured a Neapolitan Camorra organization. In Real Life, by that time all the Camorra groups in the United States had merged with the Mafia.
The Golgo 13 story "Wiseguys" has Duke Togo called in by a Mafia don over a matter of a blood feud. It opens with an FBI presentation that attempts to strip away most of the romantic myths surrounding the Mafia, and does a decent job at presenting organized crime as just prettied-up hooliganism. In fact, organized crime members are probably the most common mooks Golgo takes out, and any member whose loyalty to their boss extends to trying to take out Golgo is universally depicted as an idiot.
Verrocchio's gang in Black Lagoon; in a reversal of the common portrayals, they come off as more brutal and overall worse people than Balalaika's or Chang's gangs.
Interestingly, given that it's set in Italy, Gunslinger Girl has never shown any genuine Mafiosi. Mostly, this is because almost all of the stories happen on the boot. The Camorra do show up quite often and are either called by their proper name or The Naples/Napoli Mafia depending on whether exact accuracy or quick description is called for. The Five Republics separatists tend to act a bit like this trope (including having "cleaners"), but seem to make most of their money more-or-less legitimately.
The five republics are actually based on the most radical and indipendentists elements of the Lega Nord party
Pokémon - Although not obvious at first glance, Team Rocket, especially in the games (see below), may be based off of the Mafia. It's masked by the fact that the three you see in the anime so often are the bottom rung of the team and none of the higher-ups really give a damn about them (in fact, in one episode another member tells them their memberships have all expired), though this is no longer applicable in the Best Wishes series. In the games, you break into their bases and disrupt or (more commonly) shut down several major operations, among them two hostage situations and a (quite popular) casino. Even in the anime, the protagonists occasionally stumble across a full-scale operation. Also, you know, Giovanni (although this name was deliberately given to him in the English version).
Katekyo Hitman Reborn!. A series about a mafia boss who gets shot in the head. A lot. Him and his Harem of Bishōnen Although they're the Girlscout Mafia. The good guys, at least (I'm looking at you, Yamamoto Takeshi!). The antagonists have plans like possessing the body of the thirteen year old wimp and using him to cause World War III.
We later meet the Millefiore Family, which is possibly even worse than any instance of the mafia around today, mainly because they control the world, and their leader seems wacky enough, buthe's quite unpleasant... Or used to be...
In Axis Powers Hetalia, when S. Italy was rushing to save Spain, he ran into the mafia, who demanded that he gave them Spain's imports. S. Italy just beat them up and continued on his way. He also blames his cold (which is an in universe representation of a recession) on the mafia.
In Noir, the Sicilian Mafia is the enemy of the eponymous assassin duo in the "Intoccabile" arc. Also, one of the protagonists is the sole survivor of a massacred Corsican Mafia family (never mind that Corsica is French).
Actually Truth in Television: the Corsican Mafia does exist and is actually quite powerful and influent in France and even in other countries (though it is divided into several gangs and families). "Bouquet" isn't a Corsican name though.
Appears in Japan Inc when the Japanese have to do business in Italy.
The mafia is all over the place in Acid Town. Roughly half of them appear to be decent as far as mafia go (we're not talking Reborn here) while the other half are creep scumbags.
In Illuminati!, the Mafia is one of the most powerful groups in the game.
Mafia. Where the mafia are the informed minority versus an uninformed majority.
The Punisher's first of many victims. (The original version has his family being gunned down by gangsters for stumbling onto a gangland execution, while the version told on the one-shot MAX comic The Cell has an attempted coup go bad with both the hitman and the target's bodyguards killing the Castle family in the crossfire.)
Many of Batman's non-Cape villains. Carmine "The Roman" Falcone, Salvatore "Boss" Maroni, Rupert Thorne and Carl Grissom qualify.
The Kingpin, head of New York City's criminal empire.
In both the original comics and game of The Darkness, the main character begins as a mafia hitman. And in the comics has had a time as both an informant gone straight, and the Don. A good portion of the supporting cast and villains are connected as well.
In Astro City, the main crime syndicate is run by The Deacon. The "Dark Ages" story arc included a gang war between groups led by The Deuce, Bamboo, and Josef "The Platypus" Platapopulous.
Almost every bad guy in Sin City is a part of one mafia organization or another.
Road to Perdition deals with the Looney mob, the Capone mob, and one soldier who seeks revenge against his former bosses for betraying him and murdering his family.
Alternate Universe Fic where characters are members of organized crime (often called Mafia fic or Mafia AU) is quite popular in fanfiction circles.
The Godfather is the Trope Codifier. The genesis of the modern media portrayal, though the actual word 'mafia' was notably absent from the film versions. (Ironically, it would go on to influence real-life mafia culture, particularly the glamorous self-image that would be aspired to.) The producers of The Godfather were able to speak to a real member of the Mafia, who provided some of his 'boys' for crowd-control on-set. In exchange, he made several requests, one of which was that the word 'Mafia' be removed from the script (the director agreed, which was easy enough to do — considering that it wasn't in the script in the first place).
Goodfellas. Unlike The Godfather, it concerns itself more with the "working-class" mob, rather than the bosses.
In Snow Crash, the Mafia has become a public company and is one of many organizations competing in the marketplace of a corporate-run America. One of their most successful enterprises is Uncle Enzo's Cosa Nostra Pizza, which uses The Don as their mascot. The company guarantees delivery in 30 minutes, or you get your pizza free. Uncle Enzo flies down to your house, apologizes, and gives you a free trip to Italy. It's implied that the failed deliveryman suffers fatal consequences.
Key figures in the Stephanie Plum books, along with possibly all of the other organized crime outfits mentioned above.
The Mafia forms a part of the setting of Time Scout. They never explicitly show up, but their control of the construction industry is how they became so powerful after The Accident and helped make the present a Crapsack World.
In Dorothy Gilman's The Clairvoyant Countess, Madame Karitska finds some things that lead Lt. Prudens and the police to realize that the Syndicate is moving in, which nearly causes them to miss that there is a significant change in tactics.
The Mafia battles the Yakuza on the fifth episode of Deadliest Warrior. Al Capone's gang battles the James-Younger gang in the third episode of the second season.
On Caprica, the Tauron Ha'la'tha is an example of this, with elements of The Cartel. Oh, and they speak Ancient Greek.
The intimidating, social club-dwelling recipients of a huge roulette wheel cake on Cake Boss (filmed in New Jersey) are heavily implied to be the Mafia.
Mary's first husband in Soap was a mobster and, after his death, his son, Danny, joins. The boss, Lefkowitz, is Italian and so are a number of the other higher-ups and Danny starts believing he is too. After Danny refuses to kill his father's murderer (his step-father, Burt), Danny goes into hiding (aka. remaining where he is but changing into a series of ridiculous outfits) and Lefkowitz eventually lets him live and leave The Mafia if he agrees to marry his daughter, Elaine.
Parodied in a Monty Python's Flying Circus sketch where the Vercotti brothers visit an Army base and try to intimidate the colonel by threatening to set fire to his troops. Luigi Vercotti made a few subsequent appearances.
Boardwalk Empire has an Italian gang (a literal crime family composed of brothers and cousins) trying to move in on the rackets in Atlantic City. Important Mafia figures like 'Lucky' Luciano, Joe Torrio and Al Capone also feature prominently. The main Gang boss, Enoch Thompson and many of his allies are Irish-American whilst the often forgotten but very powerful Jewish Mafia are represented by New York Boss Arnold Rothstein.
The long-running Italian drama La Piovra (The Octopus) deals with organized crime in Italy. The title is a metaphor, comparing the Mafia to an octopus whose tentacles are in everything. Interestingly, the show gives equal time to the heroes affected by its dealings, including Detective Carrado Cattani who is killed in a hail of gunfire at the end of Series Four.
Tracker had 'A Made Guy', where the alien Zin uses the Earth Mafia to reach some of his goals, and Cole goes undercover as a mobster.
While they certainly feature, Italian novel-based crime drama Romanzo Criminale ("Crime Novel") is about a group of non-Mafia criminals.
Ellery Queen: "The Adventure of the Wary Witness" concerns the murder of the son in a prominent crime family. Mobsters also figure prominently in the plots of "The Adventure of the Sunday Punch" and "The Adventure of Caesar's Last Sleep". In both cases, it's a red herring, as said mobsters have no involvement in the deaths of either victim.
As part of his gimmick at the timenote which was "Hustle, Loyalty, Respect", John Cena's entrance at Wrestlemania 22 was a clip about the mafia during the Depression and gangsters dressed up in suits and tommy guns. He then appears dressed in a black coat and cap, as if the head of the mafia.
Werewolf The Apocalypse includes the urbane Glass Walkers, who developed strong footholds in Italy (there really is a breed of Italian wolf). And since Werewolf absolutely loves its cultural stereotypes...
The telekinetic Spooks' Guild in Wraith The Oblivion were based on the Mafia, particularly in how they were organized.
There was a mortals supplement, too: World of Darkness: Mafia.
Grand Theft Auto 3 revolves around The Mafia, and the group also shows up in important roles in the other parts of the series. In fact, Liberty City Stories has you play as a mobster who's of some importance in 3.
In IV, by contrast, The Mafia doesn't really show up until the latter parts of the game and is comparatively weak and racked by infighting, and who are ultimately played for fools by Dimitri. In The Ballad of Gay Tony, they are secondary antagonists who effectively fade into the background when Luis offs the main antagonists in spectacular fashion.
City of Heroes has the Family, who are Italian mobsters in nice suits and bowler hats. City of Villains also has the Mooks, who are just the same, except less well-dressed. Both are hilariously anachronistic as well, even the Mooks wear 20s-style fashion outfits in a Twenty Minutes into the Future world, and wield tommy guns equally as effective as modern assault rifles and lasers. Rule Of Cool, folks.
Fallout 2 has 4 different criminal families vying for control over New Reno, with 2 based in family-owned casinos, one in a bar, and the last in an out-of-ways mansion overlooking the old railway station. You can do quests for more than one at a time, so long as they don't involve killing members of the other crime families you work for. Pledging your full allegiance with one by accepting a final quest to test your loyalty will have the others permanently gunning for you. Given that this last quest tends to involve eliminating a rival family wholesale, its not too big of a deal unless you're aiming for 100% Completion.
Invoked by Mr House in Fallout New Vegas when he made over a local tribe into the Omerta casino family.
Mafia Wars lets you play a Mafia don and do all sorts of illicit stuff for cash and prizes.
Pokemon Red And Blue has Team Rocket. They're more based on the Yakuza in the Japanese version, but were adapted to be more like The Mafia in the international releases, as best evidenced by the name of their boss, Giovanni.
We also have the Mon Honchkrow, a crow that looks like it's dressed like a Mafia Don. Appropriately enough, Giovanni of Team Rocket uses one in his appearance in HeartGold and SoulSilver.
Urban Rivals has their own Mafia group known as the Montana, who make money by terrorizing the citizens of Clint City.
The Darkness and its sequel, based on the comic series of the same name, stars Jackie Estacado, a mafia hitman who inherits an ancient evil and uses it to help him fend off his crazy Uncle Paulie...who happens to be the Don.
Gangland player character comes after is three brothers, all leaders of their own families. While doing so, player establishes his own gang
In Lucky Dog 1 the main characters are part of a mafia group called CR-5. The main character, Gian, starts out as a man who is very good at breaking in and out of prison and his first job of the game is to break out himself and the four captains who all got locked away at the same time. He soon learns if he succeeds in breaking them out he gets to become the new boss.
In Sonic The Comic Online there is The Family a group of bugs from the Special Zone lead by a spider called Don Long-Legs that control the Casino Night Zone and employ Max Gamble a gangster and an old enemy of the Freedom Fighters as a "legitimate" front man.
The Mafia shows up from time to time in Survival of the Fittest, along with other organized crime groups such as the gangs in Denton, usually in the background but occasionally directly involved. For example, Antonio Franchini is the son of a Mafia Don, abducted to prove a point after the Don reneged on his part of a deal between him and Danya. In v2, Seth Mattlock's father is an enforcer for a Mafia family based in Denton, and Seth himself is not only friends with some of the mobsters but is considered an honorary member, and the mob family helps his gang when they need it (for example, when an all out gang war starts). In the former's file, Danya notes that the Mafia will probably go after him and they're welcome to try, because they won't be able tofindhim, let alone do anything to him.