We gave up on log4j under Glassfish. Instead we use slf4j (which supports commons logging api as well as its own) and logback. This keeps the application logging away from the Glassfish logs and we get a separate log file for each app we deploy rather than having them all mixed up. Check out
http://logback.qos.ch/
Hopefully you haven't hard coded log4j into your code, you're using commons logging or slf4j, right? That allows you to change your mind about the actual logging implementation later (ie using log4j, logback etc) without changing your code.
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