Hopefully I understand your question correctly...
ArcGIS Online web maps don't support the HTML popup generated in ArcMap. (FYI, ArcGIS Server 9.3.1 doesn't provide access to the HTML popup at all. This was added at version 10, I believe.)
Do you want the html to display directly in the popup window? Or simply provide a link in the popup that goes to the specific web page? I've not tried this myself, but I believe it would work to copy the HTML into an attribute field of your data. Then in the web map, you can enable and configure a popup to display the html using the single field. To display a link, you'd need to provide one field with the URL.
Thanks,
Mike