Ranked in these QuestionsQuestion Ranking
Pro Supports comparing folders
Beyond Compare can be used to compare both files and folders. File-Filters possible.
Pro Supports 3 way merge
Good overview. Clear display of changed lines (background color) and changed characters (foreground color).
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 editing files directly
Pro One license covers all major OSs (Linux/Windows/Mac)
Pro Works well with large files
Pro Can be used to compare image files
This is a useful feature for game developers using Git.
Pro Can compare remote directories
Beyond Compare can compare directories through FTP, SFTP. Also it can compare directories hosted on Dropbox or Amazon S3.
Pro Opens popular archive formats as directories
Compare archive to directory or to another archive, update ZIP archives by copying files from other side or by editing them directly in compare view.
Pro Customer Service is awesome and easy to work with
Pro Has Registry compare
You can compare Registry vs Registry or Registry vs .REG file, both local and remote. You can copy values and keys between sides or edit them.
Pro Has file conversion/preprocessing feature
You can run a script or executable based on file extension before showing a file. Great for beautifying XML, extracting text from MS Office documents, running dis-asm etc.
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.