Mission Hill had the majority of its music replaced on video. Thankfully there’s a very good restoration on MySpleen.
That 70s Show on streaming, DVD, and BR is a mess of music replacement and syndication edits depending on which version you have access to, but to my knowledge none of them have the original music despite frequent claims to the contrary.
The first season (at least) of Scrubs is missing a large chunk of the original music on DVD and streaming.
The new Netflix dub of Evangelion took out Fly Me to the Moon on every episode for licensing reasons (I’ve made a version of this new dub with the music restored myself).