In Saki, the girls from Nodoka and Yuuki's old school try to reach the prefectural finals to cheer on their upperclasswomen. They miss the train, catch the train in the wrong direction, fall asleep in the train and miss their stop... and arrive at the finals just before Nodoka's turn to play. Which also means they missed Yuuki's turn for several hours.
In the Trinity comics, Clark Kent notes that the trains in Metropolis are always on time - and that he makes a point of missing his train at least three times a week. Why? Because nobody would ever associate a guy who can't catch the morning train with a hero who's faster than a speeding bullet.
Jimmy Neutron Boy GeniusThe Movie: Jimmy misses the school bus, which gives him the perfect opportunity to test out his new bubble transport system, which doesn't work out well.
The opening of the Spider-Man movie, has Peter Parker chasing a bus down the street. Even the bus driver is in on it, since he's chuckling along with the Jerkass students and gets annoyed when Mary Jane asks him to knock it off.
The eponymous Watermelon Man "misses" the bus on purpose — he races it to work every day.
The film Sliding Doors is based on the difference it makes to this woman's life whether she gets or misses a Tube train.
Inverted in The Adjustment Bureau. Matt Damon's character was supposed to miss the bus. The problem lies in that he didn't.
The West Wing episodes 20 Hours in America have Josh, Toby and Donna miss the motorcade in Indiana, being stuck with a broken down truck, missing Air Force One due to time zone changes and getting on a train heading in the wrong direction, all so Donna can teach Josh and Toby a lesson about not losing touch with the real people they work for.
In episode "Lucky Penny" of How I Met Your Mother, Ted missed a plane to Chicago for a super important job interview. He thought it was his destiny to make it and get his dream job. He and Robin contemplate what lead to them missing that flight. Had Ted got that job, he would have had to eventually relocate to Chicago. This way he stayed in New York and met his future wife.
One quest in Vampire: The Masquerade – Bloodlines has you chased by a werewolf and just missing a tram that would have taken you to safety. It's four minutes before the tram will be back, and in the meantime, the werewolf is still chasing you.
In Shogo: Mobile Armor Division, Sanjuro tries to catch a train to cross Maritropa to meet with Kura, but he ends up missing it and having to take an alternate route. By the time he reaches her, the CMC has closed in and captured her
Cartoon Network once had a Cow and Chicken game where Cow and Chicken had to make it to the school bus on time and avoid entering a bus that had the Red Guy for a driver.
The episode "Rock Bottom" has SpongeBob and Patrick board the wrong bus and end up in the eponymous town.
In the episode "The Abrasive Side", Spongebob misses the bus by doing favors for people.
A recurring occurrence on The Simpsons, especially for Bart & Lisa to miss the school bus.
The early version of the series' intro had Bart steal the sign from a bus stop while riding by on his skateboard, resulting in the bus passing right by the waiting crowd of people standing there, forcing them all to chase after it.
Marge once tried to catch up with the bus. Otto the bus driver thought Marge was trying to race him and Milhouse commented it looked like Speed 2 with a bus instead of a boat.
Episode "Trilogy of Errors" has Lisa miss a bus to school on the day of science fair. She's desperately trying to get to school to show her project and keeps failing.
Fairly Oddparents: "A Mile In My Shoes" starts with Timmy missing his bus walking all the way to school in the rain. Just the beginning of his bad day.
ˇMucha Lucha!: It happened at least twice with the Three Mascaritas.
The first episode of My Dad The Rock Star featured Willy mising the bus on the first day of class. However, since he still hadn't been registered as a student, he probably wouldn't have been allowed in.
One episode of The Flintstones had a bus stop being moved into another location, forcing Fred and some girls to chase after the bus. Wilma believed the girls were chasing Fred.
Mighty Mouse had an episode where he offered a ride to a student who missed the bus.
In the Family Guy episode "Road to Rhode Island", Brian and Stewie's cross-country adventure begins with the two of them missing their flight home because someone stole their bags (and their tickets). The later spiritual successor episde, "Road to Europe", has a strange variation of this: they fail to get off the plane before it takes off, AND it isn't even the right plane!