Let’s get to the point.
To configure Git on Windows (under Cygwin) to use Beyond Compare 3, you should have the following in your .gitconfig file (e.g. C:\cygwin\home\<user>\.gitconfig):
[diff]
tool = mybc3
[difftool "mybc3"]
cmd = \"c:/program files/beyond compare 3/BComp.com\" \"$(cygpath -w \"$LOCAL\")\" \"$(cygpath -w \"$REMOTE\")\" /lefttitle=\"$(cygpath -w \"$LOCAL\")\" /righttitle=\"$(cygpath -w \"$REMOTE\")\" /leftreadonly /rightreadonly
[difftool]
prompt = false
[merge]
tool = mybc3
[mergetool "mybc3"]
cmd = \"c:/program files/beyond compare 3/BComp.com\" \"$LOCAL\" \"$REMOTE\" \"$BASE\" \"$MERGED\" /lefttitle=\"$LOCAL\" /righttitle=\"$REMOTE\" /centertitle=\"$BASE\" /outputtitle=\"$MERGED\" /leftreadonly /rightreadonly /centerreadonly
keepBackup = false
trustExitCode = true
[mergetool]
prompt = false