I had both: 950 2004, 990 2006 and 990 2008. I am currently and slowly looking for a 950 2005.
With the 950 I have done some 25000 miles through 15 countries around Europe with a taste of Asia and some Africa.
The first 990 was a second hand with some rust and other problems. I got rid of it after 1000 miles.
The 990 2008 is still with me, it has got over 11000 miles and it is for sale.
This is my experience and opinion:
950 is a more rude and extreme bike. It has been produced from 2003 till 2005 and each year model have some significant recalls, updates and variation compare to the previous year (http://en.wikipedia.org/wiki/KTM_950_Adventure
It is well known that 2003 and 04 models were "weaker" and had some significant pitfall. The 2005 model was consistently improuved.
The 2006-08 models had the same height specifications of the 2005 models but they had EFI and ABS. They are more realible and more street orientated.
The 2009 onwards models have the same height and a revised engine with more power. Honestly I have never ride this.
I loved more the 950. Why I am not sure. Was higher and the trottle response was more rude and exciting. Riding that bike was really exciting. My one had some consistent problems...in line with what reported from majority of people. However I know someone with 85000 miles on the clock of a 03 S model who had all the KTM recall and didn't experience a single problem.
The 990 2006-08 is definitively smoother and more performant on street. It is also more confortable thanks to a better seat. It always start at the firts click and my one has been riding ok so far. Only problem was the fuel filter that had to be replaced 3000 miles away from home.
I am not sure about all this trottle issue everyone is after. I can then tell that the 950 response was easier off road.
You really need to think to few key questions:
1) What do you want it for? Off or on road mainly?
For on road I would definitively go for the 2006 onwards. For off for the 950 possibly a 2005 model.
2)How much can you spend? The newer the more expensive!
3)How realible it has to be? The newer the better.
Keep in mind that the carb model has a 2.5 liters larger thank as the fuel pump is not integrated in the left tank. To me economy is the same, so 990 have shorter range which is ok for street trips. Also I find ABS a pain in the back when off roading. It also weight few kgs and takes a lot of useful space under the seat.
Finally I also ride a 690 enduro R. This is a completely differnt bike, much closer to an EXC than a 990. Be prepare to ride a much bigger bike.
PS. Forget about GS1200. Loads of money for a street bike.