Audio problem: At the Eiffel Tower, after Lois asks the French officer if the terrorists have the proper equipment, his voice is heard but from a side view his mouth and jaw don't move.
Sacha
Continuity mistake: In East Houston, behind the man lifted by Zod, there's a man standing several feet away from a car. A frame later he's very close to the car.
Sacha Continuity mistake: When Zod burns several cars, the street is filled with parked cars and people. From Superman's point of view the street is empty and you only get to see the three burning cars and a couple of cabs.
Sacha Audio problem: When the villains blow the people back in Metropolis, all the ones near the KFC restaurant (the waitress, the guy in the phone booth and the couple) shout or make comments but their mouths either don't move or are not in synch.
Sacha Revealing mistake: Before the villains change the faces on Mt. Rushmore, the original ones (which are a matte painting) have a greenish look. Definitely not like the real sculptures.
Sacha Revealing mistake: At the beginning of the movie, we see the three villains in front of several backgrounds. In most of these backgrounds, their outlines are fuzzy, indicating that they are actually standing in front of a green screen.
Visible crew/equipment: When the super baddies arrive on the moon and encounter the astronauts, the girl Kryptonian kicks one of the astronauts into space and you can see the strings around his waist as he floats away.
Other mistake: The phantom zone villains were captured and put in space near Krypton. When Kal-El was sent to Earth, he has to pass 6 galaxies to arrive (his father said, before Krypton exploded). When Superman sends the hydrogen bomb in Paris into space, he didn't even leave the solar system. No way the phantom zone travelled through 6 galaxies - it has no propulsion, and the shock wave from the bomb wouldn't travel that far either.
GoekhanRevealing mistake: When Zod jumps out of Perry's window he falls down, revealing its a stunt from a ground level window. The outside shots however, show Zod flying up and straight.
Sacha Continuity mistake: After Superman crushes Zod's hand, his hair gets wet and the fringe appears combed as a toupee.
Sacha Continuity mistake: When Ursa is moving the helicopter around, the sky keeps changing from sunny to cloudy.
Sacha Deliberate mistake: Luthor and Teschmaker visit the North Pole protecting themselves against the cold. Lois manages to wander around with a mere, but sexy, shirt.
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