The "divine wind" ability of Celestial dragons in the Temeraire series, which is demonstrated to be powerful enough to cause a mini-tsunami in the case of skilled users. That can sink an entire fleet of warships in one shot. Described as "not so much sound as force" the first time it occurs onstage.
The Howlers from Animorphs have a scream that plays havoc with their prey's nervous systems (the more so the more complex the nervous system).
The Mandrakes of mythology and, among others, Harry Potter, have screams of instant death.
In Maximum Ride: Saving the World and Other Extreme Sports, one of the mutant things had this ability.
Magnus has the 'Sword of the Lord', a sonic scream powerful enough to trigger earthquakes.
Zhang Fei in the novel Romance of the Three Kingdoms during his stand at Chang Ban bridge, shouted so loudly it halts the advance of Cao Cao's army. Also rumoredly, one peon DIES at the mere shout of it.
The short-lived Ace Howler in the Wild Cards series.
Drummer Boy from the later books gets a strange variant. He's a Joker-Ace (superpowered individual with obvious mutations) who got his powers soon after he got his first drum kit, which resulted in six arms and chambers in his body that produced percussion when drummed upon. He later found that he could generate hyperfocused vibration through proper manipulation of these chambers, and used this to destroy the brain of a tyrant's pet Ace.
In Catherine Webb's book Mirror Dreams, Laenan Kite weaves a spell into his scream, manipulating the pressure of the air so that glass shatters and the guards are killed.
Discworld's Agnes Nitt, AKA Perdita X Dream. She once threatened a man of screaming so hard that his brains will came out of his nose. And yes, she can do that.
The Great Shout in The Riddle Master Trilogy by Patricia A. McKillip can start avalanches (if you're not careful), knock down towers. and complete the year's nut harvest remarkably quickly if you do it right. Everybody is a potential Shouter - you just have to be sufficiently moved.
Among the famous Shouts is that vented by Queen Cyone of An on her wedding day. Neither she nor the King ever told anybody just what inspired it.
In The Runelords books the big bad Raj Ahtan gets enough voice augments that he goes from having a compelling voice to a sonic weapon capable of bringing down castle walls.
In the Percy Jackson and the Olympians novel Percy Jackson and the Battle of the Labyrinth Pan gives his panic causing cry to Grover, who uses it to help win the battle.
In The King of Katoren, the birds populating the city of Decibel have had this ability for so long that the city's inhabitants have gotten used to it by constantly using earplugs and shielding their walls and windows; Stach, the main character, notes that due to the ensuing loss of interpersonal communication across the years, the two people in town who actually more thoroughly studied the problem have never been able to share their plans and combine them into the actual solution to the problem.
In A Practical Guide to Monsters, the Yrthak (an eyeless, green wyvern with a unicorn horn) is described as being able to unleash a noise from its horn capable of knocking a foe to the ground.
In the Rainbow Magic series, Jack Frost does this by accident with the magical megaphone in Keira the Film/Movie Star Fairy's book. The day is saved with earplugs for everyone, including the goblins.