Projects (folders) are only one take on how someone might organize a set of repositories. Another is the free-form label approach. We should consider adding labels to repositories.

Update on Status

We agree that labels would help to organize, filter and report on repositories. Right now our priority is expanding Projects in Bitbucket to help organize repositories with Project Settings and Permissions. This will allow administrators to manage all repositories in a Project in one location. 

Adding labels to Bitbucket is definitely worth considering but it isn't on the roadmap yet.