Hmm, might go with 2003. The 1987 series had good action, character designs, and my favorite TMNT video game of all time was based off this version. But, I will say this was more kid friendly than the 2003 version. I liked the 2003 version since it had a more dark tone to it. It was cool when they would make the scene widescreen to heighten the suspense. The music was pretty good too (except the intro, too cheesy.) I'll probably give '03 the edge because of the storylines, and it's a closer representation of the comic books. How about you?
Btw, what's up with the 2012 series? These TMNT designs look beyond corny, but I guess the kids are cool with.....