Ooh boy, you just opened a can of worms. You're going to get all sorts of answers to this, as I'm sure all of us here have our favorites. Speaking from my experience, I'd never say one particular year, trim package, etc., is the "best". Is this what you're referring to, when you ask which "model" is better? Or are you looking at new Mustangs and are trying to decide on which to go with? I need a little clarification here.
In my personal opinion:
I will forever be in love with 1987-1993 Mustangs. My first ride in a Mustang was when I was 12 years old, in a blue 1989 GT. I was hooked. Probably the reason I don't like the body style AT ALL of the 1994-1998 (SN95) Mustangs, since that signified the "end" of the Fox-body Mustang that I knew so well. IMHO, they are too rounded, almost looking like a Grand Prix/Am in my eyes. What were they doing, trying to turn my beloved pony car into a chick-box?
I like the tough, cut, muscular look of '99-'04 Mustangs, but probably not as much as the refined retro look of the '05.