All Cobra's had the round fogs. That was the biggest difference from the front that was noticable.
Easiest things to see from the different years.
93 (4993 built)- Wing, sides skirts, grill, wheels, taillights (similar to SVO) and bumper. Colors- Teal, Red, Black. Also first year of Cobra R (107 built) which had minor differences like wheels, no A/C or radio, etc...
94-95 (11,267 built)- Front bumper, wing (similar to Cobra R), wheels, brakes, white gauges and 94 had different side skirts (rock deflector). Also only two years of "stock GT" hood, 5.0L motor on the SN-95 chassis and "MUSTANG" in the rear bumper. Colors- Rio Red, Black, White. First year of the convertible Cobra 94 which was the Indy Pace Car only available in Rio Red. 95 was only available in Black. 95 was also the second offering of the COBRA R in White which had different wheels, 351, V-6 interior, etc....
96-98- Same front bumper (since 94), twin-nostril hood scoops, wheels, brakes, white gauges, also had a regular GT wing and rear bumper said "COBRA." The beginning of the 305HP 4-valve mod motors... 96 had a small difference on the leather seats also. 98 was only year of 5-spoke wheels, different console, no strut-tower bar, no secondary throttle bodies, no more coil packs, etc... Colors 96- Mystic, Black, White, Laser Red. 97- Rio Red, Black, White, Pacific Green. 98- Black, White, Laser Red, Bright Atlantic Blue and Chrome Yellow.
99- front bumper, reverse cowl hood, brakes, wheels, tail-lights and first year of IRS. 99 had regular GT rear bumper that said "MUSTANG", same wing and side skirts as GT. HP bump to 320 but was later recalled for weak numbers... Colors- Black, White, Electric Green and Rio Red.
00- Only Cobra's made that year were COBRA R's! As most everyone knows lots....different. Front splitter, wheels, suspension, wing, RECARO seats, 6-speed, 5.4 4-valve, etc....etc.... Color- Performance Red
01- Cobra's were back with the much needed missing HP/TQ. Things different from 99 (rear wing, seats and finally said "COBRA" again in the rear bumper). Colors- Black, White, Lazer Red, Silver, Mineral Grey, True Blue, Zinc Yellow and Performance Red.
02- NO COBRA's produced.
03-04- (Differences from 99/01). Front bumper, hood, wing, side skirts, wheels 17X9, rear bumper, tail-lights, 6-speed, Eaton blower, seats, gauges, etc.... Colors 03- Dark Shadow Grey, Silver, Redfire, Torch Red, White, Zinc Yellow, Sonic Blue and Mineral Grey. 04- MysticChrome, Competition Orange and Screaming Yellow replaced a couple of the 03 colors.
Lots of mechanical changes between the different years but those are the easiest things to see from the outside....