There is a site where I use WordPress Popular Posts in the last year. On this site I have to implement a custom layout with many extra fields defined by other plugins and the theme. It's impossible to build this layout with the widget settings form.
After I examined the code of the plugin i created a patch. You can access it at pastebin.com: http://pastebin.com/303WF7mT This patch is for latest, 2.3.5 version (SVN Revision 724288)
Basically I added a filter called wpp_get_popular_posts_custom_display. If any plugin or theme implement this filter and create any output get_popular_posts() will return only this custom output.
With this patch I moved the query builder logick from get_popular_posts() into a standalon new function called query_posts().