In most cases, file i/o will be much faster and consume fewer system resources.
The reasons for using a database generally have more to do with searchability, updating and support of complex data models, not performance.
Many large sites that are built out of database-backed production systems use file-based caching for performance reasons. Vignette StoryServer, for instance, can cache page modules to the filesystem in order to avoid opening a database connection.
There are some cases where a database may be faster, but those are rare and generally would be the sort of thing you run into if you dump many thousands of files into a single Unix directory.
