HI Andy,
What a problem to have... So I have had the Nikon D200 and it is wonderful but if kit, I sold it to upgrade to a D2X. But to be honest there is not much difference. I have also had a Fuji S3 Pro in the past and this is also a very good camera. Both have the places in the photographer bag, the D200 has a 5 frames per second speed but sadly the S3 Pro is only 3 fps (this was the main issue for me). But the S3 Pro (and I am sure the new S5 have wonderful color renditions, this was a big bonus and is the main reason wedding photographers like the S3 pro.
The decision will have to be made depending on what you are going to use it for, wildlife then the D200 is for you. Portrait / landscape then the S5 is best.
I think the S5 will do 3fps, if this is the case can you live with that, that is about the same as the D50 I think. Both are going to come down I price and will make both a good option. I think and I am not 100% sure on this but is the S5 based on the D200 and has the same magnesium body
Keep me up to date on what you decide.
thanks
lee