I use DBD::SQLite for this. My cron jobs launch shell scripts which set up paths to driver programs which connect to databases, perform some work, and then exit.

The initial setup and learning curve may seem daunting (and it may be daunting for your purposes), but I've found it easier on my projects than starting with flat files and reinventing file handling and the such.

With that said, if you use something like YAML::XS to abstract away the file loading, parsing, and saving, flat files aren't too bad.