Configuring Tomcat 5.5 to redirect stdout and stderr to the web application’s log file

This is not a specific solution for Tomcat, but you can redirect the stdout and stderr in Java using System.setOut and System.setErr (http://java.sun.com/j2se/1.4.2/docs/api/java/lang/System.html#setOut(java.io.PrintStream))

If you create a PrintStream implementation which redirects output to your application log, and use it in setOut and setErr it will take away the messages from catalina.out and print them to your log.

Of course, if you want, you can always print the to both by having your implementation print the data both to your application log and to the original System.out and System.err

The cleaner way would be to use log4j or any logger api and use those API's in your application for logging.
This way you can clearly separate out the tomcat logging and the application logging.

http://logging.apache.org/log4j/1.2/