"Road to Rhode Island" originally had a scene that depicted Osama Bin Laden getting past airport security by singing showtunes after Stewie did the same thing. Amazingly enough, this episode was produced and broadcast before September 11th, 2001, when few people knew who Osama bin Laden was and even fewer knew he would orchestrate an attack using commercial airplanes. The scene was removed from future airings of the episode and even from the DVD release, although it showed up on a later "best-of" DVD note The "Freakin' Sweet" DVD set. (One could also interpret this as Hilarious in Hindsight; but given the removal of the scene, it seems to belong here.) The worst part is that the show's creator, Seth MacFarlane, was supposed to be on one of the planes that hit the World Trade Center, but was lucky enough to miss it due to oversleeping from a hangover, his agent giving him the wrong flight information, and deciding to wait for another flight (until he saw the crash on the news).
Adult Swim reran an episode where Mayor West laughs uncontrollably for about a minute straight at the name of the character Boner from Growing Pains. That's all fine and good, until you realize that they aired said episode 2 days after Andrew Koenig, the actor who played Boner, killed himself.
In one episode, a Cutaway Gag had Bobby Brown and Whitney Houston sitting in bed and asking each other simultaneously if they want to smoke some crack. Owing to Houston's drug-related death in 2012, it's just not funny anymore.
The Cutaway Gag concerning Katie Holmes escaping Tom Cruise's manor. It becomes a little awkward after their divorce in 2012 (though given rumors that the marriage was a sham to cover up Tom Cruise's alleged homosexuality, this might be Hilarious in Hindsight in a sick way).
The gag from "Blind Ambition"note The episode where Quagmire saves a woman from dying of a heart attack while Peter goes blind trying to swallow the most coins so he can get into the Guinness Book of World Records where Peter tries to do good by dressing up as "Gary the No-Trash Cougar" and threatens kids at a school with a gun has now become yet another twisted Family Guy joke thanks to the Sandy Hook elementary school massacre in Newtown, Connecticut on December 14, 2012. See also: Joe pointing a shotgun at a group of kids staring at him though his window as seen on the Christmas Episode "Road to the North Pole."
In "The Tan Aquatic with Steve Zissou", when Stewie thinks he's dying, he tells Brian to write down his final words. Instead, he draws a picture of himself hanging from a tree because he was bored and didn't feel like bowing to Stewie's whims. "Brian and Stewie" later revealed that Brian has been contemplating suicide for a long time because he feels like no one cares about him. In some viewers' eyes, this turns the visual joke from a warped one to a cry for help.
In 2013's "Turban Cowboy", one cutaway has Peter drive a car through the Boston Marathon, leaving injured, bloody bodies on the ground behind him, and is then praised for winning the race. Less than a month after it aired, the real Boston Marathon was attacked with explosives, creating a scene similar to the one in the show. Between that gag and the episode's plot of Peter joining a terrorist cell, the episode was yanked from Hulu streaming and has become the first Family Guy episode to air once before getting banned temporarily.
"Save the Clam" opens with Horace pitching for Peter's softball team and being killed when a line drive is hit right back at him and strikes him. Two days after the episode first aired, Toronto Blue Jays pitcher J. A. Happ was seriously injured under very similar circumstances.
"Road to the Multiverse" ended with Human Brian getting hit by a car and killed. This happens to the main universe Brian in "Life of Brian", killing him off for all but two episodes...and even those were retconned.
"You Can't Do That On Television, Peter": As Peter and Lois are arguing over his being too much involved in his children's TV show, spending nights out on the town and neglecting his family duties as a result, Peter warns Lois not to nag him, as he can have "any 3-year-old girl [he] wants". This typical, tasteless pedophilia joke becomes worse following the posthumous exposť on British television host Jimmy Savile (Top of the Pops and the children's television program Jim'll Fix It) revealing that he was a pedophile and only did Jim'll Fix It so he can prey on little girls.
The scene from "Airpot '07" featuring an "edited-for-rednecks" version of Cosmos: A Personal Voyage becomes this (or Hilarious in Hindsight) after a Fox affiliate in Oklahoma censored a scene from MacFarlane's reboot of the show that mentioned evolution.
The "More abandoned than James Gandolfini's workout room" gag from "Baby Not On Board". Funny fat joke in 2008, Funny Aneurysm Moment after Gandolfini died of a heart attack in 2013.
As of August 11th, 2014, the opening segment of "Family Guy Viewer Mail #2" (where Peter has the power to turn people into Robin Williams by touching them, and he attemps suicide after realizing his powers cannot be controlled), isn't so funny anymore. Said episode was re-run on BBC Three just as news broke of Williams' death of an alleged suicide. [adult swim] later pulled the episode from their schedule the next day.
The ending to "Mom's the Word" where Peter accidentally kills Evelyn by squeezing her and breaking her spine becomes this after the death of Lauren Bacall five months later.