Hello,
the most important quesion is, what Rewrite module you are using.
For IIS6, the probably best choice - or at least the one that we know that works fine - is the Isapi Rewrite 3 from Helicon Software.
This supports almost the same rewrite directives as Apache mod_rewrite, so after installation it is usually enough to create the httpd.ini file and copy there the main rewrite directives from htaccess.txt distributed with Joomla.
With other software or Isapi Rewrite 2, the configuration may be more demanding as not all of Apache's rewrite commands may be supported. In such case, the rules need to be defined manually based on capabilities of the given rewrite engine.
IIS7 has already its own rewrite engine built-in, which also is quite compatible with Apache mod_rewrite, so the same directives may be used.
Configuration details for the individual rewrite modules (that may be usually found in the module's docs) do not fall under JoomSEF support. Anyway, if you would like us to assist you with the setup and installation on IIS, you can order
JoomSEF Installation on IIS service.