I have been trying to figure out how configure beyond compare to be used via command line when using Git on windows (cygwin). Based on beyond compare's documentation they ask you to just use "path" to the bcomp.exe installation and everything should work. But it does not automatically pick up the "Local", "Base" and "Remote" params. I am using Beyond compare 3.0 PRO.
I figured out the answer with a little bit of tinkering around with the git config. Note: I edited the global git config in notepad and here's how my config looks after i was done. Hope this helps someone.
[diff]
tool = bc4
[difftool "bc4"]
cmd = "C:/program\\ files\\ \\(x86\\)/beyond\\ compare\\ 4/bcomp.exe $LOCAL $REMOTE"
[merge]
tool = bc4
[mergetool "bc4"]
cmd = "C:/Program\\ Files\\ \\(x86\\)/Beyond\\ Compare\\ 4/Bcomp.exe $LOCAL $REMOTE $BASE $MERGED"
trustExitCode = true
keepBackup = false