[http://www.winmerge.org/ WinMerge]

Example configuration, assuming winmergeu.exe is in the path:

[merge-tools]
winmergeu.priority=100
winmergeu.args=/e /ub /dl other /dr local $other $local $output
winmergeu.fixeol=True
winmergeu.gui=True

Todo: Use the regkey stuff ...