you might try using the Custom option when configuring the popup for the shapefile. Currently, you'll need to use ArcGIS Explorer Online to edit the web map and configure the popup as the ArcGIS.com Map Viewer doesn't currently expose this capability for shapefiles (it will in the future). However once the popup is configured, ArcGIS.com map viewer should display it correctly.
Other than that, you might try creating your own application with the JavaScript API.
Thanks,
Mike