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.
One episode of the Pink Panther cartoon 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...
There was a similar episode where 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.
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.
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 blackeye.
On Rugrats, Chuckie once said that the first things 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 waken 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.
Cadet offered Duck Dodgers a "Happy Cat" alarm clock for Christmas. The thing didn't last long. Can't blame the duck on this, the voice it uses to try waking you up is very annoying.
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.