Paul,
996r gets you Titanium con rods, some carbon Bodywork and Ohlins forks over a 998s.
The power quoted by Ducati is the same.
A bit of a halfway house is a Baylis or Bostrum rep, basically a 998s with a paint job and ohlins forks. There does seem a few Bostrums for sale and what I would call a good price, i.e no more cash than a 998s.
A 998r gets even more carbon and three more BHP over a 996r but I'm sure the 996r owners will be along soon to say its the best one to have 'cos it was the last of the line to win the World superbike title.
When looking for a bike or sort you mention, a good service history is Vital. If the bike is due a service budget at least £400 to get it done.
I would have a look at a few other sources other than e-bay, e.g on this board and the bike section of the online autotrader.
www.ducati.com will allow you compare the spec of non current models.
Ray
[Edited on 3-8-2005 by Ray]