The Global Guardians PBEM Universe features many characters with this power. Rebel Yell, a member of the White Legion (white supremacist hero group... yes, you read that right), has an ultra-sonic "rebel yell" as his name implies. His twin brother Johnny Reb has the same power, but not the same attitudes toward minorities. The King, the Anthropomorphic Incarnation of the popular image of Elvis Presley, can belt out ultra-powerful rock-and-roll songs. Crescendo sings into the ultra-sonic ranges as well. Golden Eagle has a super-powerful "eagle scream". Crybaby, Vox Populi, the New South Wailer, Warcy, Heuler, Screech, Grito, and the Voice of God all do the same thing.
In the webfiction Whateley Universe, there's an entire category of mutant superpower covering this: the 'siren'. At the Whateley Academy, there are plenty of examples: Vox and Glissade can imitate any sound and even make people do their bidding; Screech is so superpowered that she can't open her mouth for fear of disintegrating everything and everyone in front of her.
In Ayla and the Great Shoulder Angel Conspiracy, those three and a couple others are in a 'special topics' course in Winter Term where the whole course is learning how to do more things with their Siren powers.
It's also been pointed out that sonic weapons are for the most part illegal, because as pointed out in the main page, you can't direct them and thus they hit everything. On Halloween, the Syndicate hit the Halloween dance with a sonic attack designed to put all the students down so they can kill their targets without any collateral damage. It doesn't work.
In Darwin's Soldiers, Deathwind, a Dragonstorm experiment, can create a painful and very destructive noise by vibrating his wings. It is implied that some other experiments have the same power.
So, you thought Octocat's droning scream at the end of Part 1 of Octocat Adventure was just random? Well, in the climax, he causes such a loud, long scream that he shatters the sky and the universe.
Triumph from Worm can shout hard enough (and focused enough) to punch holes in concrete or blast regenerating monstrosities across the street.
Cricket can project sound at a frequency that lets her echolocate and induce nausea in her foes.
Shatterbird projects a combination of sound and telekinesis to control glass at tremendous ranges.
Screamer has more general sound manipulation, which she uses to conduct psychological warfare by messing with communications, giving conflicting orders, or mimicking the voices of people the targets know, and to a more normal combat advantage by screeching very loudly.
SCP-633 ("The Roaring One"). When SCP-638 is enraged it can shout with tremendous volume and force, including deafening personnel and blowing steel doors off their hinges.
SCP-1048 ("Builder Bear"). One of SCP-1048's creations, SCP-1048-A (a teddy bear made out of human ears) gave off a high-pitched shriek that caused intense pain in the ears and eyes of everyone within 10 meters. All persons within five meters started growing ears all over their bodies within 20 seconds and died within three minutes.
SCP-1420 ("Tartary Eggs"). One of the creatures hatched from SCP-1420 could produce a sound that rendered nearby human beings unconscious. It later died from internal hemorrhaging in its throat.
SCP-2812 ("Echoes of Yesterday"). SCP-2812-2 are humanoid entities that operate in the area of effect around the SCP-2812-1 record player. They have a speaker cone inside their mouths that broadcasts the same music played by SCP-2812-1, but it has a stronger effect, causing cerebral hemorrhaging in living creatures.