@Paul - he never said he was attempting to log a web application....
@Alan - I'm sure since you posted this years ago, you found your solution, however, for all of us searching/googling that may have hit on this page... I have some info to help.
First - One of the best articles I've seen written (and I've read a TON) regarding WAS logging is:
http://www.ibm.com/developerworks/websphere/techjournal/0802_supauth/0802_supauth.html
It is a good reference for IBM's recommendations, and for how to integrate JUL into your application.
Second - It is possible to log and configure logging of your application OUTSIDE of Websphere's server logs. Don't give up!
Tips....
1. Referencing the article link above, if you read WAY down towards the bottom, a KEY component to JUL configuration is this:
[quote]WebSphere Application Server initializes the logging environment based on server configuration settings rather than using the JUL logging.properties settings in the JRE/lib directory (which is the JUL default).[/quote]
Therefore overriding the Logger.properties values in the ...{Websphere Installation}/java/jre/lib location, does nothing at all.
2. Since WAS6, JUL has been the preferred logging mechanism for WebSphere, and is integrated with the Websphere Application Server logs. And, those logs will pick up every System.Out for any resource and package your application uses. You can still use Log4J, but IBM will not support or help you with logging via Log4J.
3. Websphere's documentation for your version of Websphere Application Server has pretty good documentation, if you know where to find it. Here is a link to the 6.1 version of the "Adding logging and tracing to your Application", which is a starting point, and then you need to dig deeper.
[quote][i]http://publib.boulder.ibm.com/infocenter/wasinfo/v6r1/index.jsp?topic=/com.ibm.websphere.base.doc/info/aes/ae/ttrb_addtrace.html[/i][/quote]
There is a LOT of information pages to go through, which all have benefits to how/why/what things are.
4. The page for how to set up, configure, and MOST importantly WHERE to put the Logger.properties files:
[quote][i]http://publib.boulder.ibm.com/infocenter/wasinfo/v6r1/topic/com.ibm.websphere.base.doc/info/aes/ae/rtrb_configjavalogapps.html[/i][/quote]
5. AND, last but not least.... When all else fails, and you cannot get what you want with JUL, and you want to go with Log4J or Commons Logging, here are some good places to find out how:
-- for JCL
http://www.ibm.com/developerworks/websphere/techjournal/0901_supauth/0901_supauth.html
-- more JCL
http://publib.boulder.ibm.com/infocenter/wasinfo/v6r1/index.jsp?topic=/com.ibm.websphere.base.doc/info/aes/ae/ctrb_classload_jcl.html
--
http://www.ibm.com/developerworks/forums/thread.jspa?messageID=14045904
and from that last page (is the key to overriding logging for JCL and Log4j):
[quote]
The META-INF/services approach has been working for us for years on many
different versions of WAS. (We're on 6.1 now) You don't need (or likely
want) to change the classloader ordering policy.
Just make the contents of that file:
org.apache.commons.logging.impl.Log4jFactory
A couple references:
http://www-1.ibm.com/support/docview.wss?uid=swg27010153
[/quote]
Happy Logging!