I understand people's impassioned reaction to the box-office failure of these films. But while "people like stupid stuff" explains the failure of some smart movies and the success of other movies like "Mr. Deeds," it fails to explain why good movies, like "Monsters, Inc." or, say, "The Muppet Movie" become hits.
I've done no research on the following hypothesis, so don't take it as fact, but here's what I think happened. People went to The Dark Crystal knowing it was a "Jim Henson film" -- and that's all they knew about it. If they read the reviews, if they watched the commercials more closely, they might have been more informed. But a lot of people don't take the time and effort to figure that out. "Jim Henson? That's good enough for me. I love that cute Muppet stuff." So parents around the world brought their kids to see the movie...and five minutes into it, these little creatures have their souls sucked out by hideous, large, deformed skeletal birds. Parents brought their shrieking, crying kids out of the movie theater and demanded a refund.
When Jim directed Labyrinth, he added things into the film that are absent from Dark Crystal: comedy, music, and human stars for the audience to relate to. (For that reason, IMHO, Labyrinth is a much stronger film.) But it didn't matter. Parents saw the commercials and said, "Oh, no. I remember what happened the LAST time I brought my kids to one of THOSE Jim Henson movies!" So as a result, it bombed as well.
So that's my theory, anyway. As for being too dark, Jim was, as usual, ahead of the curve -- this time, just a little too far ahead. In the '90s, we'd get Tim Burton's Batman, A Nightmare Before Christmas, The Crow, Farscape, etc. The world would eventually be ready for dark fantasy; it just wasn't prepared for it in the '80s. Keep in mind that the most successful Henson project in the '80s was Muppet Babies, which was a ratings hit and won multiple Emmys. Whenever he strayed from that path, as with The Jim Henson Hour, the audience turned its back.
And for the record, I like Muppet Babies, and Dark Crystal is a little too oppressive for me even nowadays. I'm just trying to explain what I think were factors in these films not being more widely recieved.
Hope this helps.