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As others have said, it depends: on the size and nature of the data and the operations you're planning to run on it.
Particularly for a CGI script, you're going to incur a performance hit for connecting to a database server on every page view. However if you create a naive file-based approach, you could easily create worse performance problems ;-)
As well as a Berkeley DB File solution you could also consider using SQLite. This creates a SQL interface to a database stored in a local file. You can access it with DBI and SQL but there's no server, configuration or network protocol. This could allow easier migration if a database server is necessary in the future (example: if you decide to have multiple front-end servers, but need to share state).
Without knowing any details, I'd suggest using a SQLite/DBI solution then reviewing the performance. This will give flexibility with a reasonably simple start up and decent performance.