The Project Wonder way
Project Wonder, in the ERExtensions framework, have a utility class to help you run command-line applications, ERXRuntimeUtilities. This utility class is used inside Wonder, for example ERAttachment use it to call ImageMagick when you want to resize images.
Check the Javadoc for the execute method to see examples.
The Java way
Here, the "cat" and "outputCat" are debugging output categories:
Note: A number of people have reported problems with process.waitFor() on Windows. The WebObjects Development List at Omnigroup has a number of people's workaround code for this problem.
Note 2: The procedure given here, of course, is to call anything executable from the command line from your Java program, not just Perl scripts.
process.waitFor() is not just a problem on Windows. This code will cause problems. Process maintains buffers for stdout and stderr. If you do not consume those streams, you will run into deadlocks. The proper way to use Runtime.exec is to setup a thread for stderr and a thread for stdout and consume them yourself into your own buffer that does not have the same restrictions that the stock VM has.
There's a good example of this technique on JavaWorld.