My next door neighbor owns a very well known sunroof and upholstery business in our area. I asked him about sunroofs for my 03 Mach 1 and my 07 GT. He tells me that the typical power sliding moonroofs that Ford uses in so many other products are possible in those other models as most roofs are rather flat so the glass can drop and slide neatly under the roof panel.
However, the Mustangs from 94 to the present have such a highly curved surface that the possibility of jamming and rubbing has prevented Ford from wanting to tackle a factory install and only a handful of aftermarket companies offer this kind of product. I work at a Ford dealership and we've installed quite a few aftermarket sunroofs in Mustangs, so it can be done, but the glass has to be rather short (front to rear) to keep from jamming under the roof skin.
If you don't mind a pop-up sunnroof that sticks up like a spoiler above the roof skin when it's open, then there are bigger sunroof panels that will work. But those kind of sunroofs look so 1970's!
A better alternative is glassback roof mentioned here by others. I've seen several in person and they are incredible and offer much more glass area overhead. They are spendier (roughly $2,000 to $3,000 depending on vendor), but much nicer.