Imagine a iPod/iPhone, CD, FM all-in-one sound system packed into a wooden "furniture". This may be the prototype of a physical skeuomorph. Make a new look comfortably old and familiar ..
GUIs of programs are digital skeuomorphs, if they emulate objects of the physical word. Again an audio processing software that would emulate a physical audio equipment....
They are often annoying. New media give you the opportunity to design new interaction paradigms. Take the new leap motion devices that translate gestures from hands and fingers into fine controls in a computer. You do not want to use them to turn buttons, put books on a virtual book shelf, ....
But if your softearew, like Mathematica, offers a document-centered workflow skeuomorphism makes a lot of sense. CDF - documents that look like documents but are programs.
Posting this I have been inspired by Seth Godin's blog post skeuomorph = failure.
