In Black Blood Brothers, Jiro turns off Mimiko's alarm clock by cutting it in half (since, according to Kotaro, he isn't good with new technology).
Specifically averted in Da Capo. Nemu gets Junichi a round alarm clock so that if he tries to hit it, it will just roll away and ring somewhere else.
In Hellsing, during a lull in the battle aboard the H.M.S. Eagle, an alarm clock starts ringing, only to be promptly smashed underfoot by Alucard. The alarm clock indicates that enough time has passed that Alucard will not be able to be returned to London when it is attacked by the Last Battalion.
In an episode of InuYasha, he destroys Kagome's ringing alarm clock so she doesn't wake up and find him in her bedroom.
Subverted in Lucky Star: Misao takes a damaged alarm clock in Kagami's room as proof of Kagami's "legendary morning violence", before Kagami corrects her.
In the first episode of the Pokémon anime, Ash smashes his Voltorb-shaped alarm clock against the wall while dreaming - so it doesn't wake him up at the right time, which directly leads him to get Pikachu as his first Pokémon.
In Soul Eater, the titular character smacks away an alarm clock without waking up...only to get a much ruder (or not, if you're into that kind of thing) wake-up call by Blair...
While it doesn't get smashed just for ringing (the owner was refusing to shut it off even though the signal was causing problems with a woman's medical device), Souichi grabs the phone of another rider on the train and stomps on it in The Tyrant Falls in Love.
More of a 'tick tick tick tick SMASH. CRUNCH.' and then probably stomping on the parts in Tsukihime when Shiki is getting some spillover from Roa/SHIKI and causing violent rage of which he's not really aware. He wanted to lie down and get rid of his headache so he could talk to Ciel without... getting... horrible destructive. Good luck, Shiki!
The Rare Hunters do this to Tea/Anzu's mobile phone in Yu-Gi-Oh!.
One-Punch Man: Saitama wakes up from an action-packed fight dream when his alarm clock starts ringing to which of course he punches it to stop it. Though granted it seemed it was done out of habit rather then annoyance.