For those who want a version of WordPress Popular Posts to work with WP Super Cache, please visit my post on WordPress Popular Posts and WP Super Cache.
I've tried to get a hold of the plugin author, but there is no e-mail address, and his sites seem to be down.
The "fix" involves loading the popular posts via AJAX. If WP Super Cache has cached a page, the views are still updated.
Hopefully the plugin author will see this and implement in the future.
I hope you enjoy the update.