The Daily Bugle has been around in the Marvel universe for a very long time. Established in the 1890's, it has certainly reported on a vast array of stories in it's many decades. However, like many other print newspapers, sales have inevitably dropped in the digital age.
On top of poor sales, the insurance costs of The Bugle must be astronomical. They are in New York City first of all. Second, the near constant attacks on the business by supervillains must drive up the rates. No wonder Jonah is such a cheapskate and pays his employees such lousy wages.
Let's look at all of the costumed crooks that have wrecked havoc at the venerable institution.
Alistaire Smythe
Alistaire had held a grudge against Jonah for years, blaming him for his father's death. Smythe sent an army of insect themed cyborgs after Jameson's family and friends, including Joe Robertson at Frontline. Frontline would later be rechristened as the new Daily Bugle. Hopefully they changed insurance companies after changing the name of the business. (Amazing Spider-Man #654)
Carnage
Jonah has been attacked by the mass murderer twice and somehow escaped with minor injuries. JJJ had long been a advocate for law and order in his newspaper, which infuriated the chaos obsessed killer. He broke into the Bugle with Jameson as the target, to prove that anyone can be a victim of chaos. He then kidnapped the publisher, to kill him in front of an audience. (Amazing Spider-Man #363)
Carnage assaulted him a second time at the Bugle, beating him and shredding his clothes. The killer also destroyed the "Daily Bugle" sign on top of the building, leaving only "BUG" as a taunt to Spider-Man. (Web of Spider-Man #101)
Doctor Octopus
Doc Ock has also used the Bugle for his own means over the years. He kidnapped Betty Brant in front of Jonah and Peter Parker in Jonah's office, to draw the attention of Spider-Man. Ock tossed the two men around for good measure before he left with his captive. (Amazing Spider-Man #12)
At a later date, Ock tried to extort $20 million in gems from the mayor by threatening to poison 5 million New Yorkers. It was the means of dispersal that was left a mystery. Luckily Peter learned of the threat and eventually realized that the specific number of 5 million referred to the Bugle's number of readers. He arrived at the printing press just in time to keep Octopus from poisoning the newspaper's ink. (Amazing Spider-Man Annual #15)
Years later, Octopus tried to level the building entirely with a vibrating "Temblor" device. He expected Jonah to pay him $20 million or the structure would come tumbling down, with all of the employees inside it. Spidey and the Wild Pack managed to disarm the device, which was hidden in a tunnel under the building. This was only after Ock's Temblor destroyed Jonah's statue of himself in front of the Bugle. (Spectacular Spider-Man #174 & Spectacular Spider-Man #175)
Electro
Max Dillon's episodes with the Bugle have been mostly harmless. He did kidnap Betty Brant after joining the Sinister Six, with help from Sandman. (Amazing Spider-Man Annual #1)
He also surprised Jonah in his office, offering to kill Spider-Man on live TV as the webhead was scheduled to appear on a late night talk show. (Amazing Spider-Man #82)
The evil electrician also attempted to blackmail the Bugle with the help of Blizzard. (Marvel Team Up #56)
Electro managed to destroy the building entirely after blackmailing its then owner, Dexter Bennet, for a very large sum of money. After having his name dragged through the mud by the media and large businesses like the Bugle getting tax-payer handouts to stay open, Electro decided to take down Bennet and his company. (Amazing Spider-Man #614)
Green Goblin
Norman has certainly tortured Jonah over the years, despite them being fellow country club members. Norman faked his death and let the world believe he was dead for years, until he made his comeback one Halloween. After sending anonymous invitations to various Bugle staff members, and having hired goons posing as maintenance workers lock the doors, the Green Goblin burst through the high-rise windows and announced that they were all going to die. The Goblin's men had rigged the building with enough explosives to collapse the building but they ended up blowing up the Goblin instead, only after he killed Spider-Man's clone, Ben Reilly. (Peter Parker Spider-Man #75)
Norman next tried to prove that it wasn't him that attacked the Daily Bugle, after he forced Jonah to make him co-owner of the paper. He created an impostor Goblin to prove that Norman hadn't been the one to assault the Bugle staff. The impostor attacked him at the Bugle office in front of the staff, claiming to have kidnapped Norman's grandson. (Spectacular Spider-Man #255)
Okay, bear with me. Norman discovered a mystical artifact that he hoped would give him increased power but instead drove him mad. During the fight with Spider-Man, the Goblin destroyed the Bugle, nearly causing it to collapse. It was Spider-Man's perseverance in holding the damaged building up and webbing it together that prevented it from crumbling. The same could not be said about Norman's sanity, or the quality of the story itself. (Peter Parker Spider-Man #98)
Green Goblin II
Harry was a little more subtle than his father. While he didn't explicitly threaten JJJ, seeing Harry in a Goblin costume, waiting for him in his office with an unhinged grin, made Harry's mental state very clear. Sure, he was acting friendly but considering the implicit threat, Jonah had every right to be shaking. (Spectacular Spider-Man #200)
Hitman
Then we have an obscure bad guy, like the creatively named Hitman. After serving in the army, Burt Kenyon became a mercenary and was hired by a terrorist group called the People's Liberation Army to kill Jameson after he denounced their group in his newspaper. He was a Punisher enemy and both Punisher and Spider-Man arrived in JJ's office when Hitman tried to kill him. Hitman escaped with Jonah and took him to the Statue of Liberty, with the intention of blowing him up inside the statue. Kenyon fell to his death from the crown of the statue. (Amazing Spider-Man #174 & Amazing Spider-Man #175)
Hobgoblin
It seems fitting that Phil Urich, the Green Goblin that saved the Daily Bugle from a Sentinel, would be captured at the Bugle as the new Hobgoblin. Urich stayed out of costumed super heroics for years after being defeated as the Green Goblin but a lucky break (and the degenerative effect the goblin formula had on his mental health) gave him a chance to relive his glory days as a murderous Hobgoblin. After his identity was outed on TV by the Superior Spider-Man, Urich took his girlfriend, and fellow Bugle journalist Norah Winters, hostage. Norah managed to escape but Urich used his sonic laugh to deafen the people around him, causing intense pain. Only after seeing that he was hurting his Uncle Ben did Phil relent, allowing for Spider-Man to tackle him out of a window. (Superior Spider-Man #16)
Human Fly
This is another one of Jonah's brilliant ideas that came back to bite him. He went to Harlan Stillwell, brother of Farley, and demanded that he create a superhero that could match Spider-Man. An escaped kidnapper overheard Jameson and Stillwell's conversation and after Jonah left, volunteered to be the guinea pig. The kidnapper had been shot by police during his escape from a standoff and had come to Stillwell for medical attention. Jameson later returned to Stillwell's lab and found the scientist dead from a gunshot. The newspaper man then was kidnapped by the Human Fly and held captive to draw out Spider-Man. He then attacked Peter and Robbie at the Bugle, telling them to have Spider-Man meet him at the Colosseum. Spidey defeated the pest by webbing his wings together and liquefying his insides and drinking them. Ok, he just webbed his wings and webbed him up. (Amazing Spider-Man Annual #10)
Jackal and Spidercide
Professor Miles Warren's plan for wiping out humanity and replacing them with clones was nearly complete when he arrived at the Daily Bugle. His plan involved cloning the newspaper's staff and controlling them to downplay reports of the worldwide virus that was killing millions. The Jackal was about to release the "Carrion virus" into the Bugle when he was stopped by the mysterious Scrier and Spidercide, whom Jackal had believed to be his bodyguard. The fight between Jackal and Spidercide crashed through the roof of the Bugle and the unhinged Spidercide threatened to kill the entire staff. Spidercide was defeated when he fell through a hole in the wall. The Jackal later followed his fate. But that was a clone too, so not really. (Spider-Man: Maximum Clonage Omega)
Looter
God love the Looter, but he isn't the sharpest tool in the shed. In a world where bad guys get around with goblin gliders, teleportation, and flight, he relies on a hot air balloon. As crude as his methods are, he still managed to break into the Daily Bugle to steal the $5 million bounty that Norman Osborn put on Spider-Man. He was beaten by Hornet and Flash Thompson. (Sensational Spider-Man #27)
Mad Jack
The Jack O'Lantern, also known as "Mad Jack," is yet another failed idea to destroy Spider-Man. He was the second Mysterio and naturally was beaten by Spidey. Years later, he reappeared as the latest Jack O'Lantern and began harassing Jonah and his son, John. "Jack" assaulted Jonah at the Bugle as the publisher worked late, putting him in the hospital. Later, a hypnotized John tried to smother his father in his hospital bed with a pillow. Pretty scary dealings for a guy with a flaming pumpkin head. (Spectacular Spider-Man #246)
Man-Wolf
Every parent likes a surprise visit from their kid...unless the kid is a werewolf. Thats what happened after John Jameson was infected by the moonstone and became the Man-Wolf. Seeking help, the speechless creature crashed through Jonah's office window and seemed ready to attack when Spider-Man showed up. The webhead chased the lycanthrope away, only to have Jonah threaten to tell the world that Spideŕ-Man had crashed through the window instead of the monster. (Amazing Spider-Man #124)
Morlun
It was a brief appearance, but Morlun ambushed Spider-Man at the Daily Bugle. The duo crashed through Jonah's office window and crashed around the work area before Spidey fled and the unkillable creature followed him. (Amazing Spider-Man #526)
Prowler
Hobie Brown was a young African American inventor that couldn't get people to pay attention to his devices due to his race. After being fired from his job as a window washer, he decided to get publicity by becoming a costumed thief and then returning the stolen items as Hobie Brown. He decided to rob the Daily Bugle, reasoning that if he wanted attention, there would be no better place to burgle than a media establishment. At the Bugle's safe, he was caught by Peter Parker and Jonah. Peter couldn't be seen arousing suspicion by fighting the Prowler, so he pretended to lose his balance and fall out the window. Prowler fled in horror, thinking he had just killed Peter. (Amazing Spider-Man #78 & Amazing Spider-Man #79)
Sam Bullit
Hopefully Jonah provides kidnapping insurance, as his employees tend to suddenly go missing. This is what happened to Joe Robertson after he crossed paths with Sam Bullit, an aspiring District Attorney with connections to racist organizations. After Joe uncovered those links he was kidnapped by Bullit's goons outside the Bugle. (Amazing Spider-Man #92)
Sandman and Venom
Venom took over the Daily Bugle for some reason after getting kicked out of the Sinister Six. Sandman showed up and told Spidey they should take on Venom together, after Venom tried to kill other members of the Six. Venom took a bite out of Sandman, causing him to flee. Then Spidey chased Venom away with a burning newspaper. That's it. Just a burning newspaper. (Peter Parker: Spider-Man (Vol. 2) #16)
Scorpion
The Scorpion may not be Spider-Man's greatest enemy, but he may be Jameson's. Obsessed with ridding the world of Spider-Man, Jonah hired Farley Stillwell to create a being that matched Spidey's own power. Stillwell blended the DNA of a scorpion to a human named Mac Gargan and gave him a robotic tail, thus creating one of Spidey's most unstable enemies. After seemingly defeating Spider-Man, Scorpion attacked Jameson to remove the last person who knew that Mac Gargan and the Scorpion were one and the same. Spidey arrived in the nick of time and eventually defeated Gargan after a violent battle. (Amazing Spider-Man #20)
Scorpion escaped from prison a few months later and immediately set about getting revenge on Jonah. He ambushed the publisher in his office and was about to finish him off when Spidey arrived at the last moment. The fight spread across the Daily Bugle as Jameson fled the Scorpion and Gargan relentlessly followed him. Scorpion fled and Spidey followed him after the police arrived. (Jonah commented that it all actually worked well for him, as the destroyed property was old and covered by insurance. This was very early in Spidey's adventures. I wonder if Jonah's insurance covered all of the damage sustained over the following years.) Scorpion was captured after the fight moved into New York harbor. (Amazing Spider-Man #29)
After finding the machinery at Dr. Stillwell's old lab, Scorpion returned stronger than ever. He attempts to get Jonah's attention by throwing rocks at his window, then moved on to cars. Spidey managed to catch the car before it connected to the Bugle and the obligatory fight followed. (Spectacular Spider-Man #21)
Sentinel
For a change of pace, the Bugle was once attacked by a giant robot called a Sentinel. The robots had been created to protect humanity from mutants (unnecessary as most mutants wanted to co-exist peacefully with humans) but they had been taken over by a creature called Onslaught. The creature declared New York City to be under martial law and used the Sentinels as his personal army. One of the Sentinels was sent to the Bugle in an attempt to shut down the media during martial law. The robot was defeated by the unlikely hero, the Green Goblin. (Green Goblin #12)
Stunner
The staff of the Bugle is well aware of the company's history as a super villain magnet. So when Doctor Octopus's long lost lover, Stunner, attacked the Bugle to bring out Spider-Man, no one was especially shocked. Betty Brant, who had returned to the Daily Bugle after a long absence commented that the place didn't seem the same, until Stunner punched through the wall and demanded to know where Spider-Man was. "Okay, now it feels like the Bugle," she grumbled. Joe Robertson said that Spider-Man watched the city with his spider-robots, which alerted him when a crime was underway. Stunner smiled and proceeded to tear apart the street. (Superior Spider-Man #21)
Vulture
Adrian Toomes appeared at the Bugle several times. The first time was during an attempted robbery of the Bugle's paychecks. (Amazing Spider-Man #7)
After the formation of the Sinister Six, he delivered the message to Jameson, telling him to put a notice in the paper telling Spider-Man that Betty Brant had been kidnapped. (Amazing Spider-Man Annual #1)
Toomes defeated the impostor Vulture and soon turned his sights on Spider-Man. He battled the wall crawler outside of the Bugle with Jonah and Robbie watching from the rooftop. In the fracas a chunk of masonry fell from the Daily Bugle sign and fell on Robbie. Jonah tried to help the Vulture by holding Spider-Man so he couldn't jump away. That plan worked about as well as you would expect. (Amazing Spider-Man #64)
Vulture crashed through the windows of Jameson's office to tell him that he wanted Jonah to print a headline declaring his intention to kill Spider-Man, dangling JJJ out of his window in the process. (Spectacular Spider-Man #187)