Dave, pretty much what Dibble has said (hi Dib's, hows the bike??)
The 996 has a more powerful engine (unless you get one of the 916 specials, which you won't for £6k
).
The thing to look out for is a full service history and a 1 or 2 owner model is a better bet than a 5 or 6 owner one.
Make sure that its had belts done at regular intervals and check out the general condition and spec of machine. Have a look through the archives here to see the differences between model types, you can pay alot extra for a 'tricked up' bike, but it might be hiding something, so be careful - like with anything really.
If you are offered/see one 'dripping in carbon' this that and the other, and the owner states thousands have been spent on extras - that maybe true, but it doesn't add that much to the value to be honest. If buying from a dealer, be careful, they will want top dollar for it chances are and they may not be a Ducato dealer and know nothing about them !
Some models/ages have suffered various problems, the biggest being flaking cams, but its not a model/year thing, just certain bikes suffer it, this has been discussed to death on here and the general opinion seems to be that it depends on how they are treated by the owners and whether you are just unlucky to get ones with slightly soft cams - its a real mixed box. - Don't be put off by this, we have a lot of members and visitors to this site and not many have suffered this problem and most have had it sorted under warranty anyway.
If you can find a 998 (difficult, but not impossible for £6k) then you might be better to get one of these, some prefer the 996 to the 998, but its mainly an engine thing and little in it performance wise, although the 998 is meant to be more refined - I own a 996s so I can't comment personally, but I am sure somebody here will be able to clarify that one !
check the archives and if you find one and its not on here, post the details and ask for opinions on the price/value etc, we might be a mad bunch, but we are honest !!
Mutts