I would like to know what features are available for monitoring traffic and statistics like search engine host hits. I want to use a Windows based server.

Is there a built in tool?
If I host several sites can I see traffic for the sites separately?
Are the raw log files available?

You can have AWStats on your windows accounts.

And here you have a demo on how you can monitor your resource usage.

Hope all this can be usefull for you

Yes, the stats can be viewed for your addon domains separately.
The raw logs are available in your cpanel.

Here is a cPanel tour. You can check it out on my server:
http://www.phirefast.com/cpanel_tour/tour.htm

I have been working on quite a long time ago.