I develop in PHP and C#, switching between OSX (Native Bash) and Windows (Cygwin), so I try to make my solutions as DRY and cross-OS simple as possible. For a great solution for Cygwin checkout Alexander Grob post on the same issue, mine is a slight variation of Alex's.
$ nano ~/.bash_profile DiffMerge_Path="/cygdrive/c/Program Files/SourceGear/DiffMerge" if [ -d $DiffMerge_Path ] then PATH="$DiffMerge_Path:$PATH" fi
In order to make everything cross-OS, I add the DiffMerge binaries to the Path, above is an example on how to add it to Cygwin, adding it to the .bash_profile will ensure that it gets added automatically every time I log in.