I use them for storage. They're kind of silly as anything else, really. I mean, dream visitors can't see them, only people you invite over can, and even then, you can't give them anything from your museum unless they leave. So it's pointless as anything but storage.
I was actually super disappointed to find out that the museum can't be visited in a dream. The museum should have been within the town so that it would be more fun to decorate and not just serve as a storage space. Like, what's the point of having your own exhibit if no one else can see it? Might as well just give us more closet space for storage >.<