It would depend on how interdependent your applications/projects are in the organization, and also how big the codebases are.So it boils down to how one defines a "project" in your organization. Shared codebase, shared components, shared teams, shared release cycles, could all influence how your repositories need be structured.
For simplicity, I define a project as having an independent codebase, release timeline, and/or belonging to one tool/application.If this is the case, I prefer having one repository per project. This way there is more freedom to define and implement policies/access restrictions per project.
If I had a single repository bloating over time ..I may also need to worry about the workspace checkout time etc., especially if the code for the projects are all mixed. If an application/tool/project is completed/shelved/obsoleted/migrated, there can be more control on the administration aspects if there is separation at project level.
Structuring a project repository based on its unique needs can also be easier if there is one repository per project. Each project may have specific needs, which may affect the configuration management policies (branching, tagging, naming conventions, CI etc included) followed for each project. This is not to say you cannot do all of this folder-wise within a single repository. You can. It just keeps things simpler to have a cleaner separation - that is all.
You may want to consider all these factors in order to evaluate the administrative overheads you may end up with, based on your specific setup.
This said, if the projects are all small in size, and are interdependent , requiring cross references, cross tracking, movement within each other etc., then you are better off with a single repo and one folder per repository.