Direct output into a destination file, and log any errors in a separate file:

$ jsobf file.js 1>target.js 2>jsobf.log

Pipe source code into jsobf from another program:

$ cat file.js | jsobf

Pipe obfuscated code into another program; here the jsfmt program formats the obfuscated source so you can take a better look at it:

$ cat file.js | jsobf 2>/dev/null | jsfmt

Last but not least – get the js shell from Mozilla, it’s very handy!
http://developer.mozilla.org/En/Introduction_to_the_JavaScript_shell