Freight and Setup. In my opinion, you shouldn't have to pay them. In my case, I said I'd pay full msrp ($14,995 for red) + sales tax, title, license fees, documentation. And they went for it. I know some folks on here have said that they have gotten better deals. Some people have said that they have gotten worse deals.
I think it helps if they know you are a serious buyer. In my case I got preapproved from my credit union before I negotiated the deal. And if there are multiple Ducati dealerships that you can purchase from then it doesn't hurt to check final pricing at some of them. Also, I think talking pricing in person after you have test rode the bike there is more effective also. I don't think most Ducati dealerships want to talk price too specifically on the phone with someone they've never met in person.
But then again as some people have said, the dealer does need to make some kind of profit. And you will want to be able to go to a dealership for service, parts, etc that you like the people and they like you. So, in my opinion I'd rather pay $200 or $300 more to buy from a dealer that I like more. Especially because that is only 2% of the purchase price of this bike...