The Star Trek Into Darkness DVD/Blu-ray release was somewhat feature-light. Among other things, it didn’t include any deleted scenes — but now those scenes have turned up, and you can read descriptions of them here and here.
According to Trekcore, If you purchased copies of Star Trek Into Darkness through the xBox video store, then you can use the xBox SmartGlass second-screen app to view a ton of deleted scenes that were prepared for the DVD/Blu-ray release. (And then removed from the DVD, in an apparent effort to get you to buy the film more than once.)
In one of the scenes, there’s a longer version of Kirk’s discussion with Pike after Kirk is reprimanded. Carol Marcus explains the reason for her random British accent. Uhura has a much longer conversation with the Klingons. There’s a longer fight scene on Kronos. There’s also a sequence which we glimpsed in one trailer, where Kirk falsifies his log of the mission at the start of the film, in front of his bridge crew. Kirk watches Pike die. And at the end of the film, Kirk meets the little girl who was saved by Khan’s blood — and they share a moment, seemingly indicating that they have a bond in common.
Also, there’s a scene from the start of the movie where “John Harrison” calls Admiral Marcus with a message: “He said you’d know why he did this.” And according to the film’s editors, Maryann Brandon and Mary Jo Markey, on the commentary track, the sequence was cut to keep the Admiral’s involvement more of a secret.
And for everyone who felt that Scotty got aboard the Enterprise too easily, there’s a whole sequence where he talks himself on board:
This is… shuttle Copernicus. I have the…
He thinks hard, clearly not used to this kind of improvisation.
…hull plating and the coffee cells for the food synthesizers.
His face bunches up in anticipation for getting caught.
Shuttle Copernicus, we do not have you on our registry.
He regroups, and tries a more direct attack.
What the hell do you think I’m doin’ here? Huh? You think I just happened upon an enormous box and thought I’d take a wee look? No! I’ve got a job to do! I can go back, if you like. Just give me your name, I’ll tell ’em who sent me.
A long pause. He’s sure the game is up.
Supply shuttles, you’re clear to enter. You too, Copernicus.