Speaking of The Doomsday Machine, off the top of my head I recall that a cue was missing after Spock had some dialogue on the bridge and also there was a place where Scotty was walking in the corridor of the Constellation that was different. Much like ssosmcin, I just do not have the time to sift through the episodes.
Also, the 2 episodes DVDs had a scene cut entirely in sick bay with Uhura/McCoy in The Tholian Web. It was restored for the box set release.
As mentioned, the Blu/DVD copies have sound effect changes and additions more often than music alterations.