Ranked in these QuestionsQuestion Ranking
Pro Supports comparing folders
Beyond Compare can be used to compare both files and folders.
Pro Synchronize folders
Can be used to synchronize folders. Including wildcards.
Pro Has rules for adding ignore-masks and replacement rules
So parts you don't want to see in your comparision can be hidden with ignore masks. Parts that are okay to be changed can be set with change-lists so beyond compare knows what's the replacement value and skips displaying this. So you can focus on the for you important changes. For example with the ignore mask I was able to compare two logs with different timestamps but nearly same content. (beginning with timestams the first x characters adding to ignore)
Pro Supports 3 way merge
Good overview. Clear display of changed lines (background color) and changed characters (foreground color).
Pro Can compare remote directories
Beyond Compare can compare directories through FTP, SFTP. Also it can compare directories hosted on Dropbox or Amazon S3.
Con Paid proprietary software
Beyond Compare is not free, it offers different license options depending on the number of members in a team and depending on the software version.