99-2004 GTs make 260hp and have better flowing heads ("PI heads" that the weaker 96-98 GTs didn't have). 96-98 GTs make between 215-225hp (depending on the year). The new 2005+ GTs however make 300 hp and are a 3v SOHC, and no longer a SOHC 2v motor, like all the other GTs.
All cobras are DOHC 4v motors. The 96-98 Cobras made 305hp while the 99 & 2001 Cobras make 320hp. There are no mass production 2000 Cobras, only 300 Cobra R's were made that year instead. In 2003 Cobras became power added (supercharged).
And 2003-2004 Cobras make about 420-430hp Supercharged. They are rated factory at 390 but underrated.
96-98 Cobras have a Solid Axle in the rear, while all 99 and up cobras have an IRS (independent rear suspension). The IRS is better for everyday driving and road courses, but nothing beats a live axel on the drag strip. ALL GTs have live axels
The GTs have more power down low, while the cobras make their power up high, in the rpm ranges.
Personally I would recommend getting a cobra if you could afford one. They retain their value better and the DOHC motor is a beast

However with a cobra, comes insurance problems. SOOO if you are stuck getting a GT, make sure that its a 99 or newer. Those "non-pi" 96-98 GTs are dogs, even with mods