For me the only scene that adds to the movie in the extended cut is when Donnie and Lefty have the argument in the motel room in Florida and Donnie calls him an asshle and walks out.
At the beginning of the movie Lefty is the authority and Donnie is subservient (you don't walk out on me). In my opinion it demonstrates how their relationship has developed almost as equals and that Donnie now has some real grit. The fact that Lefty just takes it on the chin even though he's pissed off seems to suggest to me that he considers Donnie a real wise guy now and there's an element of respect that wasn't there at the start. But that's just my take. All the other extra scenes I can take or leave.
So to answer your question I'm going to be contrary and say my favourite version is the non existent original version with the motel room scene, forget about it
Hey! You're not old enough to drink! Now go and die for your country!!!