Have you actually tested the penalties in performance? Depending on the size and complexity of your data, they may not be relevant.
I second all the other recommendations of SQLite, it rocks. However it is not pure perl and it does not create cross-platform, human readable data files.
P.S. I will be releasing a pure perl DBD::DBM soon but it is too early to say how it will compare performance-wise with the others. Obviously its files won't be cross-platform or human readable, but it should work anywhere that perl works with SDBM that comes with perl or with other DBMs if they are available.
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