I have a few from recent seasons... Little Women, Dracula and The Adventures of Tom Sawyer. I adore Carrie and Cyrano and a lot of other shows that were financial flops...
There is a curious paradox that no one can explain;
Who understands the secret of the reaping of the grain,
Who understands why spring is born out of winter's laboring pain,
Or why we all must die a bit before we grow again.
-from "The Fantasticks"
When I was little I loved "King of Hearts" and "Little Prince and the Aviator", although I don't know if I would feel the same way if I saw them now as a adult. I have the most vivid memories of these flops, "Smile", "Doonesbury", "Mail" "Chess" and a British flop "The Mutiny".
Little Women all the way. I saw it last December, and I had planned on seeing it again last summer, and then, like, two months before I go, I get this email saying, "Little Women is closing." I started crying.