Love Hina had a variant of this. While Keitaro losing to longtime/hardcore bowler Naru (she even had a monogrammed glove) was not presented as something shameful to contemplate, the fact that first timer Mutsumi managed a perfect game (rolling the ball two-handed the entire time) was traumatizing to the both of them.
Repeated in Mahou Sensei Negima! Long story short, through a series of misunderstandings, the class believes that Negi and Ku Fei are dating and they ended up in a bowling alley with Ayaka, Makie and Nodoka challenging Ku Fei for Negi. While Nodoka ends up getting a lot of gutters, and Ayaka topping Makie (just like Naru deafeating Keitaro), first timer Ku Fei wins with a perfect game. Unlike Mutsumi, she throws the ball with super human strength.
This was most of the plot of an episode of Excel Saga, where a bowling-obsessed terrorist group gets taken to the cleaners by Excel, using unorthodox tactics and Training from Hell. Of course, it's the kind of series where that isn't nearly the strangest thing going on.
The Prince of Tennis has the coach suggest a round of bowling on their day off...turns out that both the coach and Team Mom Oishi are frequent bowlers, and Inui decides to force those who gutter to drink his newest health drink, with the losing team having to guzzle the whole thing.
Used again in the beach volleyball episode, where the coaches outplay everybody.
Of course one has to wonder why Seigaku's players are bowling when at least three of them, including Oishi, are suffering from arm injuries.
The Big Bang Theory: A rare male on male example as Sheldon gets bested by Wil Wheaton. Also subverted in that the others acknowledge that Penny is the best bowler in the team, as she is the most physically strong. First timer Penny beating Leonard at chess fits as well.
Home Improvement: Jill bests Tim in front of all his buddies. He actually gets the final strike to win, but walked over the line. (When the game first begins turning against him, Tim tries to save face by claiming that he's letting her win because of her mother's conviction for grand theft auto.)
In The Fresh Prince of Bel-Air, there's more at stake than mere ego. Carlton is thinking about forgoing college to become a professional bowler, and his family must convince him that this is a mistake.
Step by Step: Carol and Jean-Luc beat an overly-macho Frank and his pal, Moose.
All in the Family has a variant of this, when Archie is Bested At Billiards by Irene Lorenzo.
Inverted in Kirk...when Kirk's girlfriend is the only one that can take the place of his team's star, she's terrible at it, until Kirk uses a little bit of Reverse Psychology to help save the day.
Inverted on Cheers when the gang got into a bowling contest with Gary's Old Town Tavern. It turned out that Diane had taken bowling for a P.E. credit in college, and was the best bowler on either team. Sam was so thrilled to be able to beat Gary that it never even occurred to him to be bothered that Diane, of all people, was a better bowler than him.
In a series of Garfield strips, Liz beats Jon at miniature golf.
Garfield: So what? So your girlfriend beat you at miniature golf... so she cooks better than you... so she's smarter than you... You are pathetic.
One Sherman's Lagoon arc features a golf tournament- underwater- that Megan wins. The final strip has Megan asking Sherman if he's upset that his wife, who's never played golf before in her life, won the whole thing.
The Simpsons had Maggie [the baby] beat/tie Homer in bowling. (He simply accused her of walking over the line, and docked her a point. The celebratory "300" balloon still fell from the ceiling, but Homer knocked it away quickly.)
Female example in Doug: Competent and usually level-headed Patti is beaten at bowling by casual bowler Doug; she loses a lot of self confidence as a result. At the end of the episode she challenges Doug to a rematch, giving him time to deliver An Aesop about self acceptance which she takes to heart (though it doesn't prevent her from going wild with excitement when she defeats him).
Parodied here. The girl shows up to the challenge not even knowing what sport she's playing, clearly can't handle the ball and he is athletic and clearly experienced, yet the video makes sure she hits every basket (even using an obvious male stunt double for a dunk). At the end, the lesson, as she puts it, is that movie law will not let a smug guy beat a cute girl at sports.