Aside from The Cage, (which is worthy of its own thread on this), syndication cuts, the new CGI effects, and the jigged around season one theme title music, what changes have there been between original broadcast, and VHS and beyond?
Doomsday Machine and re-recorded Corbomite and Mudd's Women music replace three opening music cues in The Menagerie, Part II. The opening teaser, (Corbomite re-recording), Act 1, (Doomsday Machine, original) and Act 2, (Mudd's Women re-recording).
An added 'sting' from the Rigel Fortress music is laid onto the soundtrack as Pike first appears in the illusion. This wasn't present on the original broadcast of The Menagerie.
The condensed Max's Factor music as Vina is restored to beauty, has been re-edited to create a smoother transition, for the DVDs and beyond, of The Menagerie, Part II.