I'm assuming you're running minecraft in a screen session, since it's the most convenient way to not force you to keep an ssh connection always open.
You can send a command to screen that it forwards to the application running inside it. For example, I am running it in a screen session called minecraft, and every few hours a script runs, forces a save, toggles autosave off, does a backup of my worlds files, then turns autosave back on.
This is how you start a new screen session called minecraft:
screen -S minecraft
then you get a shell, you may also pass the command you want to run automatically instead of getting a shell.
Then you can send commands to that session:
screen -p 0 -S minecraft -X eval "stuff save-all\015"
-p 0 sends the message to window 0 in the session
-S minecraft is the session name
- the rest tells to print "save-all" and a newline to the application's stdin