I've finally done it in this way.
Added a ServletContextListener that does the following:
public void contextInitialized(ServletContextEvent event) {
ServletContext context = event.getServletContext();
System.setProperty("rootPath", context.getRealPath("/"));
}
Then in the log4j.properties file:
log4j.appender.file.File=${rootPath}WEB-INF/logs/MyLog.log
By doing it in this way Log4j will write into the right folder as long as you don't use it before the "rootPath" system property has been set. This means that you cannot use it from the ServletContextListener itself but you should be able to use it from anywhere else in the app.
It should work on every web container and OS as it's not dependent on a container specific system property and it's not affected by OS specific path issues. Tested with Tomcat and Orion web containers and on Windows and Linux and it works fine so far.
What do you think?