Question: I am looking for compare utility similar for "win merge" or "beyond compare" .
That in addition for gui comparison will have api that i will be able to run on my files via my code and see if the files are the same or not and also use it in gui mode to show graphically the differences .

Any recommendations ?

thanks

Answer: 
If you're looking for a Diff API (as opposed to a standalone tool), try [DiffPlex](http://diffplex.codeplex.com/).
Beyond Compare 3 does support command line actions, so you should be able to hook it into any existing process that you have.

Here's the command line documentation, if you're interested:
<http://www.scootersoftware.com/help/index.html?command_line_reference.html>

Free versions are available for download.