"Most visited" probably was computed based on history. I'm not aware of any way to "undelete" history. Do you make regular backups of your computer? If so, perhaps you have an older version of places.sqlite, the database file that stores bookmarks and history. Restoring that is a little bit risky, so a fresh backup would be in order first.

With respect to downloads, how were they deleted? Or was it the downloads list (download history) that was deleted?