Beyond Compare can be used to compare both files and folders. File-Filters possible.

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)

Good overview. Clear display of changed lines (background color) and changed characters (foreground color).

Can be used to synchronize folders. Including wildcards.

This is a useful feature for game developers using Git.

Beyond Compare can compare directories through FTP, SFTP. Also it can compare directories hosted on Dropbox or Amazon S3.

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.

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.

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.