If you can find one in the same condition as a GT, its probably a good deal. I would guess the ones going for less than a GT are in bad shape somehow. The SGT, as I understand, comes with the FRPP handling pack ($1400), Hurst Shifter ($200), Shelby Grill ($300), Le Mans Stripes ($400?), CAI and tune ($700), Borla Muffs ($300?).. and I am sure there are some other things that I cant think of right now. It was a good car. I would buy one over a regular GT if they are the same or comparable price. You can buy a GT and all the parts, put them on yourself... but you dont get the Shelby name, and it might take a while to get all the parts on the car.
I have had my GT for about a year now, and am just now getting into Shelby GT type of performance. However... I have modded slow because I spent as much as I could on the car itself at the original purchase. If I were to do it again, I would buy a cheaper car, and then immidietly spend 2-3k on bolt ons.