The 'Scrubs' episode "My Life in Four Cameras" isn't lost but the first time it aired I remember you got to hear the opening theme of 'Cheers' in the third act and it really went well with the sitcom theme of the story. In subsequent airings however this was removed, for some legal reason I assume. Wish they could have kept it in.
On a similar note the Sopranos season 3 episode "Army of One" had a different actress playing FBI agent Debra Cicerrone when the episode first aired- Fairuza Balk, but for whatever reason she got replaced with Lola Glaudini for all future airings and home releases(either because she wasn't able to commit to the series or because the creators thought she wasn't convincing enough in the role) some of her scenes showed up on Youtube but not all of them.
I heard there was also an episode of Seinfeld where one of the characters fathers was played by a different actor at first but then changed later on for re-broadcasts and home releases.