I normally use java.lang.ProcessBuilder and java.lang.Process to run external command line programs, and it works fine for run-and-done commands. For example, this would run
Redirecting stdin and stdout is certainly one option for simple command-line programs.
Using a "robot" class is another, if you actually need to script keystrokes (for example, in a test script):
http://www.java-tips.org/java-se-tips/java.awt/how-to-use-robot-class-in-java.html
http://download.java.net/jdk7/archive/b123/docs/api/java/awt/Robot.html
Writing a simple .bat file or shell script, that calls your Java program and uses "<" and ">" redirection operators is yet a third option.
It all depends on exactly what you're looking for :)