UPDATED…
I want to call kdiff from Console application. So I’m building two files and want to compare they at the end of executing my program:
string diffCmd = string.Format("{0} {1}", Logging.FileNames[0], Logging.FileNames[1]);
// diffCmd = D:\vdenisenko\DbHelper\DbHelper\bin\Debug\Reports\16_Nov 06_30_46_DiscussionThreads_ORIGIN.txt D:\vdenisenko\DbHelper\DbHelper\bin\Debug\Reports\16_Nov 06_30_46_DiscussionThreads_ORIGIN.txt
System.Diagnostics.Process.Start(@"C:\Program Files (x86)\KDiff3\kdiff3.exe", diffCmd);
//specification is here http://kdiff3.sourceforge.net/doc/documentation.html
It runs kdiff3 tool, but something wrong with filenames or command… Could you please look on screenshot and say what is wrong?

You need to use
Process.Start():Arguments as described in the docs:
kdiff3 file1 file2