I'm wondering what is the app that used to make this kind of these videos/screen-casts with awesome 3d effect.
I found these two videos which I guess both made using the same app.
They don't use any one app. I'm guessing they first change the desktop background to green and capture the screen with some screen capturing app, like Quicktime X for example.
They record and then they edit the video in either After Effects or Apple Motion, where they can key off all the green and make it a "3d layer". They take a screenshot of their windowless desktop and throw it behind the recorded window, maybe add some soft lights to create a dim shadow and after that its all a mater of playing with the camera.
In After Effects or Apple Motion you can also make the effect of "switching between monitors", like on the kickoff video. You simply put it all inside another composition, that atop the picture of a Macbook air, and then move it all together. You can think of Apple Motion and After Effects as the "Photoshop" of videos: you can make pretty cool stuff with them. I use After Effects ;)
I agree with @kevin9794 that these videos have probably been done in AfterEffects. Please note that the "Analog" video is technically more advanced: the Mouse cursor is a separate item that has all properties of a real 3d object: depth, shading, generates shadow etc.
If I had to do it, I would do it like this:
Not quite easy, but certainly manageable with a bit of time and attention to detail.