Your question would be better off in Seekers of Perl Wisdom. See Where should I post X? for more information.

There are lots of ways to make graphs with perl, but I am not sure what you mean by a "stacked graph". Do you mean a graph of stacks (i.e. a stacked bar chart), or do you mean a stack of graphs (i.e. multiple graphs displayed in layers). Assuming you want stacked bar charts, you might look into GD::Graph or Chart.