In A Day in the Life of a Commissar, a Dawn of WarMachinima, Commissar Steeve does this when he's told Galactic Starbucks is out of coffee. He stops to ask "Really? What kind?" once he's told that there is, in fact, some coffee left. And finishes when he's told it's decaf.
In Deserving, everyone has No Indoor Voice especially when uttering the word "no", which appears in ALLCAPS as often as not.
In Revenge Road, Kyosuke wakes up after realizing that the previous events, Hikaru killing him and Madoka was All Just a Dream. Madoka then gets up to answer the door, like she did before, and when Kyosuke realizes what time it is, he runs down the stairs yelling "Midnight? Oh no! Madoka! StOP! NOOOOooooooo!", only to find that he is too late as Madoka gets shot and the fic ends.
This occurs twice in Oh God Not Again; once by Fred and George when they see the Quidditch field is now a hedge and again by Harry when he finds out Hermione won fifty points (again) after he dedicated himself to losing the House Cup.
In Losing Control Voldemort and all of his Death Eaters yell one when Azrael announces that as punishment they'll have to spend the next thousand years serving Muggleborn as house elves.
In Harry Potter and the Fold Harry yells one after a nightmare where the shades of Cedric and his parents say he should've died in their place and the figure coming out of the cauldron after Voldemort's resurrection is himself.
In Nobody Cared Snape yells one during a nightmare about Remus almost killing him during his sixth year.
In Save Our Souls the Patil twins' mother yells one when she thinks something happened to them.
In Emancipation Hermione yells one when Macnair kills Crookshanks.
In Snape's Worst Nightmare, chapter 7 ("Them v Us"), Snape lets out a huge "NO!" when Isabella Weasley manages to get the Snitch in a game between the Weasley-Potter team and the Slytherin team. He had bet Harry that he would never punish the Weasley-Potter cousins if they won.
A meta example from Harry Potter and the Methods of Rationality: Early in the story, based on the Quibbler headline about how Harry gets Malfoy pregnant, the author got several e-mails asking if Luna was a seer, and if the story was going to turn into an HPDM bottom!Malfoy mpreg fic. The author regretted that fanfiction.net did not allow a larger font with which to say NO.
In The Circle Fred and George yell a deliberately melodramatic one in unison when Dumbledore announces the cancellation of Quidditch at the start of Harry's fourth year.
In Harry the Hufflepuff 2 Harry yells one when the conductor of the Knight Bus realizes that he forgot to switch the bus out of "night mode" and all of the beds are replaced with uncomfortable-looking wooden chairs.
Nyx's dramatic "No! No no no no no NOOOO!!!" in chapter 3 of Past Sins definitely qualifies, not to mention her many other Rapid Fire Nos.
In the Tamers Forever Series The Nightmare does this when struck by Gallantmon and Sakuyamon's Dual Force: Spirit of Chaos technique.
Justified in that he was most likely screaming in terror and pain.
For a more humorous example (ironically in the Crapsack World of the Dark World arc), when Twilight asks The Voice whether it's some repressed part of Discord fighting against himself, it replies with one of these loud enough to leave her cross-eyed and temporarily aphasic.