If you run your WAR with tomcat/jetty plugin pass debug options to the Maven:
export MAVEN_OPTS="-Xnoagent -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000" mvn tomcat:run
If you run your WAR using the regular Tomcat, just run it with JPDA (debugger) support enabled:
$TOMCAT_HOME/bin/catalina.sh jpda start
Default port for Tomcat 6 JPDA is 8000.
Now connect with the Eclipse (Debug -> Remote Java Application) to the port 8000 and enjoy your fine debugging session.