When Tomcat is run via Eclipse the logging that is normally set up in the the catalina.bat or catalina.sh strat-up scripts is not set up. This is because Eclipse handles the setting up of the server and by default doesn't setup the logging. I find this very frustrating because during development logging is a very useful tool. To turn on the log manager (note: this only works with Tomcat 5.5.9 or above) add:

-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager

to the run configuration of the server.