Continuity mistake: Zod throws the Sheriff's rifle away and it lands next to the wheel. When the angle changes it has moved behind the wheel.
Sacha
Continuity mistake: When Lois is making an orange juice the position of the oranges differs between wide and close shots.
Sacha Continuity mistake: During the scene where villains arrive to the Daily Planet, Jimmy Olsen's haircut changes from long to very short.
Sacha Continuity mistake: When Clark comes back to the diner to take revenge, a dish next to the bad guy suddenly appears.
Sacha Continuity mistake: When Super arrives at the Daily Planet to defy the 3 villains, the outside shot shows three piles of books lined along the window. From the inside, all of the books are piled to the right. Also, the number of trophies on the bookshelf on the right, and the type and number of books changes between shots.
Sacha Continuity mistake: At the end of the movie, in the diner, the bad guy's food keeps changing appearance.
Sacha Continuity mistake: When Superman reveals his identity to Lois, the liquid in the top of the lava lamp changes from filled to empty in half a second.
Sacha Continuity mistake: After Superman throws Zod against the ice wall, Non's position changes between shots: First he is way behind Luthor, and a second later both are side by side.
Sacha Continuity mistake: When Non enters the Daily Planet there's a wood shelf with four sheets of paper, the ones in the middle are yellow and the rest are black and white. When the shot changes to a wide angle, all the papers are black and white.
Sacha Continuity mistake: When Ursa sits down to arm wrestle, coasters magically appear on the table.
Sacha Continuity mistake: When Non rampages the Daily planet, the grey file cabinet lying on the floor changes positions before and after he enters.
Sacha Continuity mistake: Superman descends to stop the big truck from exploding and lands in front of it, by the cabin. A frame later he is seen landing a meter before the truck.
Sacha Continuity mistake: When the antenna is about to crush the pram, the mother is first behind it. A second later she's by the side. Then a second later she's on top of it, and a second afterwards slightly covering it. Boy she moves FAST.
Sacha Continuity mistake: Inside the Fortress of Solitude, when Non jumps to fight Superman, before he flies, Ursa and Lois are looking at Superman. A mere frame later, when Non starts to fly, both girls are in a different position fighting against each other. It's a really awkward and sudden change.
Sacha Continuity mistake: At the end, in the Fortress of Solitude, Lois' hairstyle keeps changing from fluffy and dull to smooth and stylish.
Sacha Continuity mistake: After the hide and seek game in the ice cave, Luthor's fringe constantly changes length and style.
Sacha Continuity mistake: Clark steps out of the diner and the waiter has his hands on his chest. A shot later his hands are on the counter.
Sacha Continuity mistake: After being hit by a cab, Lois calls Clark and the people behind her change in a split second.
Sacha Continuity mistake: In the big fight scene in Metropolis, after Ursa chokes Superman, Non descends and wires holding him is visible.
Sacha Continuity mistake: When Superman is about to stop the elevator, he flies with one arm up the other down. A frame later in a new angle both arms are up.
Sacha 
Answer: There's been no categorical statement, but given that the theatrically released Lester cut is the one that everybody knows, with the Donner cut being a relatively unknown curiosity, it would seem much more logical to consider that the Lester cut to be the canonical version of the story.
Tailkinker