There is very little difference from the command line. I move back and forth during the day from Debian to OSX terminal without thinking about it. Unix commands, Bash, Perl and Ruby scripts all run the same way.
That being said, if you are EXPLORING from the terminal you will find major differences once you drill down into the subdirectories, since OSX is built on BSD Unix and Linux is a Unix clone. For instance, if you try to find rc2.d in /etc on OSX so you can change start up programs, like in Debian, you are out of luck - you have to find the OSX/BSD documentation.
But, looking at both from the top of the tree, they are mostly the same, with the usual home, etc, dev, sbin and other subdirectories (not folders) being recognizable.