I usually shoot in Aperture priority mode and have the viewfinder set so I see the ISO in the viewfinder. Without taking my eye from the viewfinder I can adjust ISO and Aperture and I really like being able to pick both and to do it quickly (the D7000 is my first Nikon and the first camera I've had that let me see ISO in the viewfinder and change it so simply).
So I've not used Auto ISO and I'm uncomfortable with the idea. I will add that I'm very comfortable going up to 3200. I think the D7000 really controls noise well. I'd also add that I will shoot 6400 if I need to, but probably shoot RAW to improve my ability to remove the noise later.