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It would also be interesting to know how many of those IIS sites are just companies Outlook Web Access and MS Terminal Services gateways. Lots of things will serve you some HTML over port 80 that aren't what we think of as "web sites".

Yes -- the vast majority of IIS implementations are run behind corporate firewalls -- they won't show up in surveys like this. These stats don't show web server popularity, they show the popularity of public web servers.

Even public is debatable, many web application servers or servers requiring accounts likely won't be hit. The percentage of all HTTP requests that are to servers they measure will likely be pretty low.

Very good observation. Netcraft is not measuring internal corporate servers. It can only measure what it can reach -- publicly accessible domains.

Would be interesting to know just how many of those exist.