I actually watched the whole trilogy in the last two days, and the first is definitely the best. Though the interaction of the turtles gets amusing once you accept how immature it is. (they are, after all, only 15 year olds). The second was just too goofy with a lot of uncalled for yelling and such -- though the guy in the tutle suit does some much more impressive "chucking" than in the first. the third improved on that drastically by keeping the absurdity, but toning it down. Also, they got Cory Feldman back to do Donatello and had Casey Jones again. Yay!.
The best bit in the whole trilogy has to be
*Raphael is disarmed but still beats up about two dozen ninjas
"You guys must be studying the ABRIDGED book of Ninja fighting."
*Raphael beats up a couple more ninjas.
"I mean, come on. How do you guys expect to beat me?"
*several dozen more ninjas show up
"Good answer!"
The remainder of that scene is also very amusing. with lines like "He likes it" (cut scene to Raphael being dragged down the stairs) and "Guys, I'm not so sure that, structurally speaking, this is such a good time for your friends to drop in.