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.
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