Here’s how to start Skype minimized under Linux. Install gdevilspie (it needs python-glade2 also, be sure to install it first), then run it. Add a new rule:

Start devilspie and click on the checkbox to start devilspie automatically on startup. Devilspie will be added to the Gnome startup application list, edit the entry and change the command from devilspie to devilspie -a.