[Nickj]

Hey Rob one of the primary things to look for is the round black things at the front and back, just as in Scootaboys avatar LOL

Seriously the S2R's aren't that old and I don't think thay had any major problems.
So you're looking for history, a full set of keys (blacks, red and a code card) and general condition. Service is important, pretty vital are belt changes at 12K ish or 2 years, you really don't want to have one let go on you. So a 4 yr old bike should be on its second set of belts regardless of the miles it's done. Don't walk away if not just factor in an adjustment for the £xxx service costs (or £40ish DIY)
Ducati seem to have problems in mixing making sticky casing paint so some chips is OK, lots with much bubbling round them not so good and a bargaining point. The horizontal cylinder takes the brunt of the abuse and often you find flaking there.
'Extras' add limited value but do look nice.
Miles, well if underused the battery suffers and the owner won't have made an effort to make sure it works in all conditions so you can get irritating gremlins related to dry or slightly corroded connectors. That's the same on any bike though.

Ideal is a papmpered toy that's done about 2 - 3 K a year with regular services.