For a while it would have been my other '86 GT (had it in 1995, 60K miles, all stock, great shape, but some rust), but then in 2004 I bought my current '86 GT, which had more miles, but is just a nicer car.
So I'd have to say my 1993 Cobra. Had 45K miles in 1996, I was living in Biloxi, MS at the time, active duty Air Force. Bought it from some guy over in Alabama. He had only changed the exhaust. I was really new at modding cars, so I didn't even touch it. Owned it for about 6 months. Some stupid c*** hit it in a parking lot, right out in front of my barracks. Messed it up pretty bad in the back. From the day I bought it, I had this SP (Security Police) on me about selling it to him, so as soon as it was hit, I asked him if he wanted it. It wasn't the same after it had been hit, and I was really having a tough time paying for it and the insurance on my measly Air Force salary. So I sold it. I don't really regret selling it, but it would have been nice to keep it because those damn cars are so hard to find in nice shape for a decent price. I'd love to get another one, but I just don't want to pay the asking prices for a nice, not beat on, 1993 Cobra...
Here's a pic:
http://www.wease.net/pics/Cobra1.jpg