Just my 2 cents...
I work on a Windows system with Perl 5.6.1. I've used Perl with MS Access, MSSQL Server and mySQL using DBD::ODBC and DBI. As others have said, let the data drive your choice of a database, as well as the availability of said data source and your personal preferences. Perl works equally well with any and all of the ones above.
I actually started out with an Access database because that was what I had on my PC at work and also what I was most familiar with. Problems on my out-sourced server required that I port everything into MSSQL. After moving my data, it was a simple thing to change the DBI references and the code continued to work perfectly. Later I moved some of the database info to an internal server and ported it into mySQL. Again, a quick change to the DBI references and all was well.
I say all that to say that even if you decide on a particular database at this time, that won't have to be set in stone. It's fairly easy to convert data and have perl come along with the changes. For simple database work, I prefer the mySQL. It's readily available, portable across systems, isn't Microsoft and is fairly user friendly.
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