This is my personal understanding about the topic.
For a project, we can do the version control by different repositories. And for a repository, it can manage a whole project or part of projects.
Regarding on your project (several prototype applications which are independent of each them). You can manage the project by one repository or by several repositories, the difference:
Manage by one repository. If one of the applications is changed, the whole project (all the applications) will be committed to a new version.
Manage by several repositories. If one application is changed, it will only affect the repository which manages the application. Version for other repositories was not changed.