I've used both the Nikon and Imacon and there are a few differences but the biggest one to me is the speed and quietness of the Imacon. Secondly, I think the Flexcolor software is a little easier to use than Nikon Scan, Vuescan, and definitely easier than Silver Fast. Third, if you are on a Mac there seems to be a bit of trouble using Nikon Scan 4 when there are any other Firewire devices attached to the scanning computer. I've had to switch to Vuescan on certain occasions for that reason, though I prefer how the scans look with Nikon Scan.
I own the Nikon 9000 only because it was what I could afford at the time. If I could afford it, I would rather have the Imacon. Actually, I would rather have a Fuji Frontier so I could batch scan entire rolls, but that's another story.