For small databases (under 250 Gb), the difference isn't crucial in most cases. When the application reaches a certain size, you have to look at "scale out" versus "scale up" and start spreading the load across more servers. Some types of data such a pictures, audio, video, and complex multimedia will perform much better if you allow easy parallel access by storing them in a file system.
An application that I worked on a few years ago is a great example. There was a fair bit of conventional database activity which was hit directly by the application servers. There was a fair bit of multimedia that was served directly to the web servers by the file servers. By picking the right persistance (storage of data) for the task at hand we were able to both increase performance and decrease the cost of the solution at the same time.
Databases are my preference for storing true "data" that can be edited by the user or that is used for making decisions about processing. File systems are still much better for static information such as application help and video tutorials.
-PatP