Max: Mind if I drive? Sam: Not if you don't mind me clawing at the dash and shrieking like a cheerleader.
Also, in first episode of the second season, Bosco screams like this in response to the word them. Sam even gets a dialogue option to repeatedly say "Them!" just to freak him out. Admittedly, Bosco has a very good reason to freak out, as we learn in the last episode of the season.
In Infinite Space, Ian apparently did this offscreen when he and Torlo evacuated Rhea (whom they thought dead until she suddenly moved). He is not pleased when Yuri and Torlo mock him about it.
BlazBlue. If you use the English voice, in Ragna's Gag Reel, after being informed that he's a ghost, the very thing he feared, he screams like a little girl. There's no girly scream in the Japanese voice, though.
Glottis: There was this one high-pitched whine it was making — really grating noise, you know? And I searched and searched, but I couldn't find the source of the noise, until we pulled in here. Velasco: Was it the blower? Glottis: No, it was Manny screaming in the back like a cat tied to a cruise missile!
Blood. Caleb screams like a little girl when he dies. Or is set on fire.
Caleb:AH! IT BURNS! AH AH AH AH AAAAAH!
Dragon's Lair. Dirk the Daring does this a number of times, but most noticeably in one "miss" sequence during the "Crypt Creeps" scene with what looks like black goo.
The manager of the Sedgewick Hotel from Ghostbusters: The Video Game screams like this, which the Ghostbusters at first mistake for a woman. He does it whenever a ghost appears throughout the level, and eventually faints.
Alistair of Dragon Age: Origins confesses that he used to do this while dreaming of darkspawn and the Archdemon: "I screamed like a little girl. Duncan thought I had someone in my room." He also demonstrates girly screaming in a banter with Shale, attempting to give Shale an idea of what pain feels like.
Elh of Solatorobo hates bugs and screams when they get too close. Of course, given that she is a girl, it's more understandable, but Red didn't know that at the time.
Kaos in Skylanders Trap Team shrieks in the cutscene that plays after you've cleared the Time Town level, when a character who mentions travelling into the future pulls out a large watch. To be fair, he did spend most of that level stuck to a cog wheel in the clock tower.
Disco Kid in Punch-Out!! for the Wii has a high pitched, unmanly yelp when he gets a Star Punch in the face. His normal speaking voice is about an octave deeper than the sound he makes after getting an uppercut to the jaw.
Any of the dinos in Trog, should they fall off the edge of the island.
If someone smashes through their enemy's gate in Rock of Ages, the enemy commander inside the castle will emit a girly scream as they stare down the giant boulder. It's reasonable, given given what's about to follow.
In Fire Emblem Gaiden's fully voiced 3DS remake Fire Emblem Echoes: Shadows of Valentia, Celica's friend Boey has a rather morbid fear of Terrors. He seems particularly frightened by the game's Necrodragon enemies and there are at least two instances where he lets out a high-pitched shriek when he's confronted by them.