Well according to the official site they're:
TMNT 2
Features:
Widescreen and full screen versions of the film
5.1 Surround Sound
Stereo Surround Sound
English subtitles and Closed Captions
"Pick That Flick" game
Additional DVD-ROM content
TMNT 3
Features:
Widescreen and full screen versions
5.1 surround sound
Stereo surround sound
English Subtitles and Closed Captions
Theatrical trailers
"Pick That Flick" game
Additional DVD-ROM content
Dunno what the 'additional dvd content' might be