U cant use pngs directly as icons...and yes ico files will take all the good things off the pngs like transparency.... so if u wanna use png for icons on the desktop or for launcher then u can either use Avedesk or ObjectDock/RocketDock/RK launcher/YzDock etc.....
I think AveDesk can do this. It removes all windows desktop icons and replaces them with 'Desklets' which can have PNG's as icons alongwith configurable alpha values, shadows, etc.