The Funniest Scene (in my opinion) is when Donatello is hanging onto the Neutrino's car and gets his shell scrapped against the building. Later, Michaelangelo adds some turtle wax to it
The other funny scene was one that i mentioned in a thread on here. It's Leonardo playing an Arcade game while the Turtles hide out. Very rare, but funny Leonardo.
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Donatello: Pork rind.
Donatello: Yeah, a few inquiries.
Donatello: Turtles don't migrate, Raph. Birds do!
Donatello: Have you seen the way this guy drives?
Donatello: 0.00000003%!
Donatello: I don't know, but it doesn't look good...