What am I doing with all my VHS and Laserdisc Trek episodes? Keeping them. I always have the need to watch a lower quality print. :-) Besides, it's become something of a museum in my house, along with my Mego Trek toys.
Back when the first DVDs came out, some episodes were missing things; The Doomsday Machine omitted the music when Kirk says "I'm gonna ram 'er right down that thing's throat."; The Tholian Web was missing a chunk when McCoy discharges Uhura. There are music and sound effect mistakes and substitutions galore throughout the 40 original DVDs.
The season sets featured corrected prints of The Doomsday Machine and Tholian Web omissions, but the rest of the sound issues remained, and do so to this day on the Blu-Ray releases, even though the first season has a nearly correct original mono sound mix to choose to hear the proper music and effects.
However, the Columbia House and Paramount individual tapes and lasers had their own problems. We're all familiar with the City on the Edge of Forever music substitution, which was thankfully rectified for DVD. However at least two episodes (one from each set) was missing lines of dialog, but are complete on DVD and Blu-Ray.
The restored print of The Cage on DVD and BD is missing the line from Pike re: Vina "you were like a wild little animal."
The BD's ain't perfect either. The alternate mono sound mix is great, but the main credits music for WNMHGB has an edit. The original first season theme (the Alexander Courage arrangement with the electric violin thingy) is not on the first few episodes, as on the DVDs, and none of the episodes aside from WNMHGB includes that version of the end titles. No home video version ever did. At least one episode has the new redone opening sequence on both the "remastered" and "original" effects prints, but I think there's more. The mono sound mix in the second season still has the exterior engine rumble, which was discontinued mid-first season. I haven't checked the third season episodes yet.
As it stands, there is no "absolutely correct" version of the series out there. All of them have changes and differences which remove them from the network versions. The laser discs come pretty close, but they standardized the opening theme in the first season, plus the episode previews from the first two years were changed from a superimposed NEXT WEEK graphic over the scene, to the "Next Voyage" clip with second season Enterprise shot.
Of course, you only care about this stuff if you're as anal as I.