Actually, the "commands" are the same, because the userland tools are all the same (usually by GNU).
The default shells are usually different though. I believe FreeBSD defaults to CSH, where linux defaults to BASH.
BSD was derived from actual UNIX, where Linux was started as a clone.
They both have real UNIX in them though, as they share code, and much UNIX code was open sourced.
The big difference between BSD and Linux is that one group develops both the kernel AND user tools. FreeBSD develops their own kernel, OpenBSD theirs, etc. Where as a linux distribution generally uses the generic linux kernel, and just modifies the package list, installer, GUI tools, etc.