Just out of curiosity, which scene was missing from the two-episode version of The Tholian Web? Was it something with McCoy on the Defiant? Also, not to get too off-topic, but - Doomsday Machine background music in The Menagerie? That seems rather bizarre.
I never owned most of the two-episode DVD's, I basically upgraded from the VHS tapes straight to the season box sets on DVD.