I have lots and lots of notes spanning many many topics. Folders are somewhat helpful for organization, but it would be really nice to have some higher level of separation similar to 'Spaces' in Confluence, or 'Notebooks' in Evernote. Each 'space' could have its own folder hierarchy, but would isolate its contents from all other spaces in the UI.
This feature would also open up the possibility of expanding Paper's Templates to collections of documents and folders.