Cost of goods sold are DIRECT costs of producing goods sold. They are almost always inventory related (items purchased for resale or items purchased to make manufactured goods).
That said. The shipping fee is clearly a selling (or administrative) expense - it is not a DIRECT cost.
I have seen companies post what you refer to as the application fee to either a cost of goods account or an expense account. Some like to use the cost of goods account because it helps them keep the direct costs separate from the indirect costs. I think either way you do it will be okay - the tax preparer will place it in the proper place on your tax return.
Kathy
