diffoolにWinMergeを使う

.gitconfig

 [diff]
tool = winmerge
 [difftool "winmerge"]
cmd = "'C:/Program Files (x86)/WinMerge/WinMergeU.exe'" -e -u -dl "Base" -dr "$REMOTE" "$LOCAL" "$REMOTE"
 [difftool]
prompt = false

WinMergeコマンドラインオプション

http://manual.winmerge.org/Command_line.html