In Glassfish v2.1 I could look at my web-applications log all stdout and stderr in the glassfish server log ($GF_HOME/domains/domain1/logs/server.log). But I dont see the sa
http://blog.saddey.net/2010/03/27/how-to-deploy-a-grails-application-to-glassfish/
This tutorial very succinctly explained what the problem was and fixes it, at least for grails applications which is primarily what we deploy to glassfish.
In the v3 environment, System.out and System.err get sent to the log file... via a logger.
The logger's name is "javax.enterprise.system.std.com.sun.enterprise.v3.services.impl".
A message to System.err is logged at Level.SEVERE. A message to System.out is logged at Level.INFO.
You may want to start the server and verify the log level for "javax.enterprise.system" in the admin console. It is the last logger named on the page in this screen shot, right above the 'Save' button.
If this logger is set to OFF, no messages will get to the log file. If the logger is set to SEVERE or WARNING, messages to System.out will not get logged.
EDIT: Added screenshot
In order to see the System.out.print() messages, you should set javax logging level to INFO.