The Venture Bros.' own Brock Samson did this in his college years to Rusty's alarm clock, mostly just to show how intimidating he was.
Eddy of Ed, Edd n Eddy has been known to pummel his alarm clock on occasion.
One time it shows that Eddy has a pile of smashed up alarm clocks in the corner of his room.
The episode of the Pink Panther cartoon "In The Pink of the Night" starts with an alarm clock waking the titular character up. Pink tries to turn it off, but it keeps going anyways. He reaches under the bed for a mallet and pummels the clock into submission. He then gets up and puts the clock into a drawer that was already full of broken alarm clocks...
In the same episode Pink first smashes the alarm clock using a massive wrench (from a drawer full of wrenches), then cuts the cable to his radio alarm (with clippers from, yes, a drawer full of clippers). The episode was then dedicated to Pink's new cuckoo-clock. Hilarity Ensues.
Seen in Snoopy, Come Home, when sleeping in Woodstock's nest on their journey to see Lila in the hospital, Snoopy is startled awake by his very loud alarm clock, and smashes it with his fist. Then Woodstock begins chirping in his sleep, so Snoopy conks him on the head as well.
Bart Simpson does this to his alarm clock in the song Deep Deep Trouble from the album, The Simpsons Sing the Blues.
In one episode of Hi Hi Puffy AmiYumi featuring the girls' stay at a farm, Yumi is woken up by an alarm clock modeled after a rooster. She smashes it, then goes back to sleep; however, a REAL rooster lands in the open window and issues an even noisier wakeup call, to which her response is less than polite ("You stupid turkey!").
At the end of the episode "Cat Nap", Kaz and the girls' pet cats simultaneously smash an alarm clock each with a different hammer.
In the classic Warner Brothers' cartoon, "A Bear For Punishment", Junyer has a whole table of alarm clocks. When they all go off simultaneously, Pa Bear frantically tries to shut them off one after another. Junyer silences the whole array by putting a finger to his lips and "shushhing" them.
Two other Warner cartoons have an alarm clock violently silenced at their conclusions. "Porky's Badtime Story" has Porky bashing the clock with a mallet; its remake, "Tick Tock Tuckered" has it getting shot dead.
Although no clocks were harmed, one Popeye cartoon has Popeye doing everything he can to keep Swee'Pea from waking up, including punching out music students, crushing several cars, and sinking a ship.
In an episode of Undergrads Nitz has stupidly told Kimmy Burton that he has a travel clock with an assload of features. While he's trying to find a clock to buy on the internet Rocko shows up and has nowhere else to go. Rocko decides the two of them should spend Friday night getting wasted rather than looking for a clock. Nitz doesn't drink and spends the whole night worrying about the clock. When he wakes up an hour before he meets Kimmy to give it to her he realizes he's fucked and Gimpy tells him to relax and it's on its way. When it arrives he goes to get ready to meet Kimmy. But since it's a travel clock designed for different timezones the alarm goes off waking up a hungover Rocko. Nitz returns to the room to find Rocko smashing it with a bat. Later, when Gimpy messages for help over the computer, Rocko holds up the same bat and say "Smash?"
In another episode, Rocko is woken from his stupor by an annoying noise and reaches out to smash the alarm clock... only to remember he doesn't own an alarm clock. He opens his eyes to discover that he actually smashed the keyboard for his computer, and the noise is coming from downstairs.
The rooster variant is the entire point of the Tex Avery cartoon "Cock-a-Doodle-Dog".
On an episode of Jimmy Two-Shoes, Lucius does this to Samy, who's acting like a human alarm clock.
In a Mainzelmännchen (from ZDF, the 2nd German TV channel) toon the alarm clock strikes back...the Mainzelmännchen ends up with a black eye.
On Rugrats, Chuckie once said that the first thing his dad did when he woke up in the morning was throw the noisy clock against the wall.
In one episode of the 90's X-Men series, Wolverine was shown being woken up by an alarm clock and instinctively destroying said clock with his claws. He then remarks that he hates when he does that.
In the 2001 parody on Animaniacs an alarm clock wakes up the Warner brothers a bit early, so Yakko reaches out of his stasis pod and smashes it with a mallet from across the room.
Rocko's Modern Life took this to the extreme in "Day of the Flecko," when a feather from a passing bird lands on the Bigheads' station wagon while Rocko is trying to sleep in after working all night, setting off its' very loud car alarm. As if noisy alarm wasn't enough, Bev Bighead orders Ed to shut the alarm off by completely demolishing the car, and the smashing sounds don't help Rocko either.
The 1941 Donald Duck short Early To Bed is basically 7 minutes of Donald VS. his alarm clock, followed by Donald VS. his sofabed, then the revenge of the alarm clock.
The 1988 reboot of Beany and Cecil opens straight away with an alarm clock going off and coming apart at the springs on its own.
Road Rovers has Shag constantly being irritated by his alarm clock going off every five minutes. The final time, all the viewer hears is an irritated growl, a Dramatic Gun Cock, and an explosion. We then immediately cut to Shag sleeping soundly while holding a smoking missile launcher, with a crater where the alarm clock used to be.
Arthur: In "Slink's Special Talent," Slink doesn't want to wake up at 6:00 AM for his paper route. He hits the snooze button on his alarm clock and tries putting it in a drawer before becoming frustrated, at which point he swats the alarm clock off his night table and across his bedroom.
One episode of X-Men: Evolution features a variant: Kitty Pryde phases her hand through her alarm clock. Her phasing power disrupts electronics she passes through.