I'd very much like to know how specifically the surround mixes and/or "original broadcast" audio tracks on the Blu-rays differ.
Well, to document every single change in the sound mix would be a huge undertaking. Let's just say that certain music cues were substituted (The Menagerie Part 2) or added (The Deadly Years), while others used different takes of the original cues (The Doomsday Machine). The sound effects were changed across the board. Pilot and early first season bridge sounds were added to the mix in every episode; the Enterprise exterior engine rumble was added to every episode; photon torpedo sounds were added to Balance of Terror; "sliding door" sounds were added to the Klingon torpedo hits in Errand of Mercy and the memory beam in The Paradise Syndrome; the laser beams in The Cage vary in volume during firing and it is VERY annoying.
Really, seriously, it goes on and on and on. The Blu-Ray mono track for the first season seems accurate, but the 2006 version of the main theme is used at least once, the "cello" theme is used where it shouldn't, and so on. The mono tracks for the 2nd and 3rd seasons still have the engine rumble.
The sound mix is so thoroughly screwed up it will never be the same again. The VHS/LD mix isn't perfect either, but it's much closer to the original.
If anyone has 16mm prints of the episodes, those would have the original "night of broadcast" sound mix. To my knowledge, no alterations, other than the title of the Next Week preview, would have been made for prints sent out to for initial syndication.