I came across a handy little application called DiffMerge that allows you to compare multiple files and make changes while open.  This is extremely useful when comparing multiple MikroTik configuration files.  Previously I used sdiff, but I think this is much easier to use.

DiffMerge

 

 

DiffMerge is a free application and can be used on OSX, Windows, and Linux.  The download can be found here.

http://www.sourcegear.com/diffmerge/