After the start of the call move the mouse pointer to the area under the photo. Select the item zobrazit číselník in the menu call.

After you click to zobrazit číselník, the keyboard appears.

The keyboard button is in another place in Skype 4.0:

In older Skype versions, like 3.8 may be the keyboard hidden somewhere else, but you don't have to look for it.
Just press the buttons on your numeric keypad when you are prompted.