IIS7 & IIS7
Most IIS7 settings are held in the web.config files in the root folders of the web applications and virtual folders. These can be compared with any text diff tool (albeit the XML format means two equivalent files could appear very different just by re-ordering nodes).
To get the list of virtual directories, web applications and application pools you need to use the command line tool
C:\Windows\system32\inetsrv\appcmd.exe list apppool
will list all application pools.
IIS6 & IIS7
In this case things are not so simple. An export of the metabase is a completely different format.
One option might be to the use metabase export, and on IIS7 install and IIS6 metabase comparability (use web server role options to select this) and then compare the export output.