The NEX-5 has a slightly larger grip than the NEX-3, and it's just large enough to feel comfortable, but a little insecure for one-handed shooting because of the limited places on the back for your thumb.
The flash comes off, and also tucks down flat on top of the camera.
If you look at the right side of the LCD, you can get a sense of how the contextual controls work. Pressing the indicated button will bring up the virtual mode dial, and scrolling the wheel will adjust aperture size. Notice how you get both a numeric aperture readout as well as the iconic closer-farther indicator. Also notice how low the battery's getting; the camera has pretty lame battery life.
Don't worry, you can make this display a lot less cluttered.