I also have worked with ISS. I had been using Nessus for some time, so I had a handle on what shows up from a scan. ISS did find some things that Nessus did not, most or all were in the areas of Windows Registry key permissions and Windows system privileges. However, Nessus found a lot that ISS did not.
If I had to pick just one of them, regardless of cost, Nessus is the clear winner. However, if I had to have a backup scanner as a sanity check, ISS would be a decent decision. The _Network Computing_ article (referenced earlier and on the Nessus web site) is a pretty good article and worth reading if one is looking at comparing the various scanners.
