We run a few WordPress blogs on Windows IIS using ISAPI_Rewrite for the permalinking. Everythign works fine.
The only main issue is when you create a Page in WordPress it generates the Permalink as domain.com/page/ This can cause problems with ISAPI_Rewrite as you then need to add a rule for each page you create.
Personally I think a better solution would be to have the ability to create a Page prefix like you can with the category prefix. Then you can build a rule around this prefix and therefore not have to create a rule for every page you add.
So you coudl add the prefix /pages/ and thent eh URL would be domain.com/pages/page/ then a simply /pages/(*) rule can be used in ISAPI_Rewrite and no CSS links or anything similiar are broken.