Hello,
we have always runned JoomSEF with Helicon's ISAPI Rewrite module.
V3 is ideal, as it support the same rules as Apache uses, so no changes are needed. (except maybe so small adjustments if using free version)
As regards the other options, they can cerainly be used as well, but you will need to adjust the Joomla .htaccess rules so they work fine with the specific rewrite module.