Alright, I havn't seen it in like 3 weeks. That damn bunny scared the shit outta me, so ya know...Anyway, heres how I thought of it.
At the begining of the movie, Donnie ecapes death a few times. Then Frank, the scary ****tard freak rabbit person (who is also his sisters boyfriend) tells him about whats happeneing. He starts to see into the future, or he's on acid. Either or, they both make sence. At the end of the movie, after his ****buddy dies, and he kills Frank, he travels to the spot where he first woke up (at the begining of the movie) -- This is where he see's the time portal. The plane that his mom and little sister are on blows, and one of the engines falls. Since they already lived through all that stuff (the whole begining of the movie) when the plane engine falls through the time rift, it goes BACK in time to when it origionally hits. It comes down, kills Donnie (but if you notice he has a smile on his face, because he knows whats going to happen, and what would have happened if he stayed alive)
Also, if you notice, Frank (at the end of the movie) is holding his eye or puts his hand to his eye, showing that he knew something was going to happen to it. The mom and the little girl (Donnie's **** buddy) had some sort of unspoken bond. The two teachers (Berrymore and Wile) were in some sort of a bad mood (or it looked like it) -- so on and so forth.
Hope that clears anything up. I'll watch the movie when I get home today, and I'll make any corrections and tell you the rest, because I know I'm forgetting something.