It's worth what it's worth to you. Offer them what you'd pay. The worst they can say is "no".
Keep in mind that Munroe Motors is a good Duc shop, and building a relationship with a good shop can be almost priceless. Read some of the horror stories on this board with folks having major problems with their bikes...most of the time these problems are brought on via incompetent mechanics, either themselves or someone else. Food for thought.
Yeah, I was looking at those two bike too. They look to be in great condition. I'm thinking of waiting till 07 to see what Ducati comes with. If I don't like the new superbike then I'll get a 998 since they'll be depriciating a lot more.
I'd think that is a little high. I know of at least one guy who's bought a 998 for that price or less with less than 5k miles and in near mint condition.....Three years ago, I passed on a 2000 996, locally, with 5500 miles with an asking price of $6500 in near perfect shape. The guy only had it to tour the parking lots (2" wide chicken strips on the rear tire). I still wish I had the money for that bike when I saw it. Amazingly, it took them nearly three months to sell it at that price.
Might be just a touch high, but remember that is a dealer price. So, you get the added peace of mind and legal recourses over a private party sale, plus they have to make a little bit of a living too. Anytime people ask about a good price, folks jump in with their, "well I got a GREAT deal" stories. Those are not really the norm and buying what very well may be a basket case from some guy who doesn't know what he has is comparing apples to oranges with a properly prepped bike from a dealer. Sometimes the risks are worth the reward, other times people get burned.
First off ask yourself, how many 996S's are out there with under 3K miles? If you want a very low mile bike, and especially an S or R model, do you even have much by way of options? Is this the dealer's starting point for negotiations (i.e could you get it for less or with some gear and accessories thrown in)? You might be able to find one for $1000-1500 less, but have to make a weekend trip to get it. What is sacrificing your weekend, a night in a hotel, meals on the road, and a few tanks of gas worth to you these days? And remember that it might not be all that was promised when you actually get there, so even the expense of the trip is a risk. I would think a local bike sale would be worth up to $500 over a driving distance bike sale, and probably even more over a deal for which you pay shipping and risk buying unseen. Plus the previously mentioned quality dealer relationship.
Guess what I'm saying is you really have to evaluate what it's worth to you. If that is the bike you REALLY REALLY want, what other choices are available to you? Weigh the pros and cons of each of your options, plus waiting for more options. The price to me seems not unreasonable for a fairly rare bike in so close to new condition. Especially if they are willing to negotiate a little.