The 998s & 998R models are both very desirable, the "R" being the best of the two.
If you down the 998s route get a genuine monoposto as only 27 of them came to the uk.
As bungi said, the 998s & 998R are very different engines despite the small difference of 3 bhp, the R has a larger bore and a shorter stroke. I cant actually remember if the 998R is actually 998 or 999.
However you choose I`m sure you will enjoy the Ducati experience, by the way there are a lot of funny people in the club that will try and convince you that yellow bikes are quicker than red ones, this of course is complete and utter rubbish and as any owner of a red machione will tell you, the yellow is actually an undercoat that needs a red top coat to complete the bike.
.................................mines a scotch & coke thank you.