It has recently come to my attention that the version of "The Cage" on Blu-Ray was in fact not the original version, and there is in fact some material left out. The following is what I believe to have been changed.
-Many of the effect shots appear to have been desaturated in the Blu-Ray version. No idea why.
2003 DVD version
-Big one. Malachi Throne's original voice for The Keeper. Pitch-shifted for The Menagerie. The original was heard in the 1986 restoration's black and white footage, but not the Blu-Ray where the remaining dialogue was pitch-shifted to match the Menagerie footage.
-A brief music sting added for the Menagerie has gone unnoticed in all versions except Roddenberry's 16mm.
-A few frames of footage in the briefing scene, including Spock switching the monitor off, are missing in the 1989 restoration. (Although the monitor is back on in the last shot of the scene)
-The picnic scene is missing some shots. To fit the existing color footage to the uncut soundtrack, some shots are repeated. Additionally, both the 1986, 1989, and Blu-Ray are missing some dialogue present in the original 16mm print.
-Before Pike's line "Don't help me. . . They can't read through hate", the Keeper exits the menagerie. After that line, a shot from a later scene of the Keeper returning is re-used. This was made to cover up the dissolve to the later scene that was made for "The Menagerie". Originally, this shot followed a closeup to Veena, a cut to the Enterprise bridge, and a cut to the prisoners asleep in the cage.
-A brief portion of dialogue was edited out here as well.
-After Pike beams back to the ship, there is a reaction shot of Number One and Spock. The color print of this shot was lost, so what is used instead is a re-photographed shot of the shot played on the view screen (taken from The Menagerie). This is evident because the shot begins to pull back and we can see the edge of the monitor screen.
Just a little thing showing how the Blu-Ray version is incomplete and rather strange in terms of coloring and editing choices.