Since OS X comes from a unix heritage, you will want to store system files in
/usr/local/bin for command line applications and scripts that belong to the system locally and not to a specific user. You may need to create this directory first by running:
sudo mkdir -p /usr/local/bin
You can move any command line application to that folder by running:
sudo mv my-binary /usr/local/bin/
To make sure that
/usr/local/bin is part of your standard search path in Terminal, check the content of
/etc/paths and add it if necessary:
grep -w /usr/local/bin /etc/paths || sudo sh -c 'echo /usr/local/bin >> /etc/paths'
Some users make a second directory for user level scripts, but this is even more subject to personal preference.
I typically make a bin directory in each user folder and then hide it from Finder - but you can make that decision yourself whether you want it hidden:
chflags hidden ~/bin
In this case, you'll want to have each user's path include this location by modifying the shell startup scripts (
~/.bash_profile for bash which is the standard shell)
or by hard coding the path to each app when you run it.