Yes, I'd like to see that eye for detail examine the differences between the various versions of the episodes. The DVD and Blu-ray editions of the episodes have small alterations here and there that I've noticed while rewatching the series via Laserdisc. The music cues are different in places for The Cage and even in The Menagerie. There's also a notable music splice in A Taste of Armageddon that's always bothered me.
For me, the most egregious omission is Spock's "He'll do it" line from the end of The Trouble With Tribbles - I have loved that line since I was a kid and it drives me crazy that it's not on the DVD.