I do know that there are some limitations with Spreadsheet::WriteExcel and the author of that module acknowledged two such limitations just yesterday (Spreadsheet::WriteExcel and type=line/area), but I don't know what all of the limitations are since I don't use that module.

Personally, I primarily use Perl in Windows. As such, I use Win32::OLE to control Excel directly from Perl. As Corion pointed, that does require Excel to be installed. Basically, anything that you can do manually with a mouse and keyboard in Excel, you can do with Win32::OLE and Excel.

As for your scenario (running on a Unix based system), it sounds like Spreadsheet::WriteExcel may be the better route to go since Excel is a Windows only application.