The destination fee is usually considered a non-negotiable item that is in addition to the invoice price. Some sites roll that item into the invoice, but Edmunds tells you what the number is. Other fees include document fees and ad fees. Both may be legit but any doc fee over $50 is suspect. Ad fees are negotiable too - why should you pay for the dealer's advertising? That's a cost of doing business.
Optional equipment can be negotiated, perhaps down to dealer cost and perhaps below that. And some equipment can simply be removed and the whole price reduced.
However, instead of trying to negotiate the various fees (and most of them are negotiable), I suggest that you focus on your out the door price (OTD). That way you'll spend your energy on the final number and you shouldn't have any surprises when you get ready to sign the papers.