A similar question was already asked, but for Ubuntu.
It would help to know if the tool is free as in beer or as in liber.
Also, up and downs of the tool would be nice to know.
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On Windows, a good 3-way diff/merge tool remains kdiff3 (WinMerge, for now, is still 2-way based, pending WinMerge3)
See “How do you merge in GIT on Windows?” and this config.
Update 7 years later (Aug. 2018): Artur Kędzior mentions in the comments:
If you guys happen to use Visual Studio (Community Edition is free), try the tool that is shipped with it:
vsDiffMerge.exe. It’s really awesome and easy to use.