I've never used DBD::Chart, but for scatterplots at my job we tend to use GnuPlot. We even use it through Perl, though the module we use (Chart::GnuPlot) doesn't seem to exist on CPAN. If you're working with the output from another application already, though, it's not clear that perl is doing more for you than just gluing things together, so GnuPlot might work on its own.

The GnuPlot FAQ also points to PGPERL as an option, though I know nothing more about it than that, so I can't provide any more useful commentary about it.

Good luck!