Here’s a rough list I made of movies that have been ruined by stereo (specifically ones that have had intrusive new sounds added). Feel free to add to it.
007 films: The films from Dr. No to The Man With The Golden Gun have all had additional foley added to their stereo “remixes”. Thankfully, they also include the mono mixes on the Blu-Ray.
The Godfather (Parts I and II): Some sound effects have been changed in more recent releases.
H.B. Halicki’s entire filmography: Not only have they ruined the sound effects on DVD, but several scenes are missing from Gone in 60 Seconds.
Dirty Harry series: Enough has been said about how much these films have been ruined, so I’m not going to say anything.
An American Werewolf in London: In addition to the annoying new foley effects, the entire soundtrack has been pitched down!
Thunderbirds: The classic Gerry Anderson series was remastered in stereo in the late 90s. Unfortunately, they added additional sounds to the mix (sometimes not very well, as you can still hear the original sounds underneath). The 50th Anniversary set released by Shout! Factory includes the mono soundtrack, thankfully.