Quite of few of the folks we work with that use nimbusql use the scheduling feature. Just like a saved search scheduled email, but would use for anything too complicated for a search.
I like your idea for the folder structure, think we'll add that in as well. Currently I've been using the notes field to "Tag" when saving a query, then using the table searcher to find something with the tag, but the folders would be a good way to organize and use the tags for more generic categorization.