Also the amount of money makes a big difference. The 03-04 cobras are generally regarded as the best all round car aside from the 05+ machines.
What are your power goals? What kind of driving do you want to do, racing, drag, twisties? And finally money?
Generally the 96-98 GT unless you love the look are the worst years. They make less power and have less support, although a head swap takes care of the majority of that.
The 99-04 GT are the most common. There is ton's of support. But the power will never be the same as a cobra without some serious money spent. A few grand to play with the big boys.
The 99 Cobra is IRS instead of solid axle like the GT's, it is also a 4v instead of a 2v, however, it does not have a power adder like the 03-04 cobra's. The 99 is a great car, but not quite as much out of box potential as the 03-04 cobra, but more potential than the GT.
Any of these can be modified to do whatever you want ofcourse, the main thing is. How much performance do you want stock? How soon will you be able to do mods if you plan on doing them? What looks the best to you?
Don't buy an 96 because its cheap and you plan on modding it, if its going to take 3 years to afford moding it. Take the hit in your monthly payment and get a newer car that won't upset you with its performance. That being said, if you have $4k in cash to drop on the car after you buy it. Go for it, for 4K you can build it up to haul ass and depending on your direction, you can get a nasty suspension set up, or push the power a good bit.