The 2011 Blu-ray version replaces the Yoda puppet with a computer generated Yoda.
The 3D release of the Phantom Menace features the Blu-ray cut of the film, which includes the CG version of Yoda. The 20th Century Fox and Lucasfilm logos in the beginning of film are updated with more 3D effects.
There are two versions of the climactic finale where Darth Maul is killed by Obi-Wan Kenobi. In the original, he is seen falling down the reactor shaft, dead but in one piece. In the updated version (in general release), he is seen falling down the shaft in two pieces, cut in half at the torso. Apparently, original press screenings presented the first version, but the second version is what most people will see to make it clear that Maul is dead.
At the very end of the final credits, after the closing music has faded out, the sound of Darth Vader breathing can be heard. Reportedly, this sound was not in the prints of the film shown during pre-release press screenings.
The DVD reinstates footage into the feature and increases its running time by 3 minutes. Restored footage includes the Coruscant air taxi sequence, extended starting grid sequence and extended lap two sequence.
In the theatrical version, right after Sebulba's name is announced in the podrace opening, there is a shot of Watto, in his booth, cheering on Sebulba with joy. On the DVD, this scene has been omitted from the actual movie on disc 1, but is still present as part of the "extended podrace sequence" on disc 2.