I'm a pretty big fan of Frank Wildhorn's shows, even though lots of American critics and "serious theatre fans" like to bash him. I adore Jekyll & Hyde, The Scarlet Pimpernel, and Dracula despite their flaws, and I also quite enjoyed Rudolf and Count of Monte Cristo, though I don't know those two as well as I think I should, and I've never seen any of his shows live. I wasn't as fond of what I heard from Wonderland and Bonnie and Clyde, but I still have great respect for Frank as a person and an artist, and it bugs me when people tear him down for hypocritical or nationalistic reasons. I'm glad he's seeing some success in Europe and Asia, though.
Another one I adore is Stephen Sondheim's Assassins. Like many of his shows, it had a rather short run on Broadway but got lots of critical praise. Even many Sondheim fans seem to think of it as a "problem show," but it's possibly my second favorite of his shows after Sweeney Todd.
Chess is another show I love, and I do hope it gets a really great stage production someday. And if we can count Sunset Boulevard despite it being a Tony winner, I'd go for that as well -- possibly my favorite ALW show, period. I also loved what I heard from Side Show, Lord of the Rings, and Next to Normal. And I shamelessly adore Repo; I've only seen the movie, but I'd love to see how it's done onstage sometime. And this one's definitely not "unliked," but the stage version is far less well-known than the film -- Disney's Hunchback of Notre Dame. It's only been done onstage in Germany so far, but that production managed to be darker and more faithful to the novel than the film was while still keeping the fantastic music and adding to it. Definitely an example of a screen-to-stage adaptation done right, and I hope that it's done well if/when it's brought to Broadway.
Now, for a major, major guilty pleasure of mine (and at the risk of any credibility I might have previously had)... Spider-Man: Turn Off The Dark. Specifically the version in previews before Julie Taymor was fired -- I thought the narrative device of establishing that the whole show was fanfiction by comic geeks actually worked in the show's favor for me (since then I wasn't bothered by out-of-canon or out-of-character changes or the fact that it was more an adaptation of the movies than the comics), and so I was a bit sad that that whole thing was cut from the show before the official opening. In all, though, the show was poor but didn't offend my sensibilities either as a comic book fan or a musical theatre fan. If tickets had been considerably less expensive, I might have even been willing to see it live... I had kinda hoped it would be filmed and released on DVD, but it looks like that didn't happen.