There is obviously subjectivity here, but for my money, the following immediately came to mind:
Chess (On the the best scores ever for me, saw two boring productions and a decent one (at the Signature in northern VA)
Merrily We Roll Along (Only saw two productions...the original (as bad as the legend) and on in Boston five or six years ago. It was much better, but still not as good as listening to the OCR)
Mack and Mabel (great score, deadly production)
The Roar of the Greasepaint (great score, show simply too 'precious'
On a Clear Day (not a great score, but infinitely more enjoyable than the show)
Fun Home (loved the score, disliked the show a lot)
The Band's Visit (loved the score, found the show lethargic)
Titanic (Great opening, downhill from there)
The Great Comet (I thought the staging was a terrific gimmick; even with the staging, I think it is better listening to than seeing, at least based on my viewing of the original production. That may be due to the fact that I appreciate the score the more I hear it).
SITHWG: I have never enjoyed the show as much as the recording, regardless of the production. I have always found that Act 1 dragged; I have loved AND hated different stagings of Act 2. Hated the original Act 2, loved the version at the Roundabout, for example.