Your web application should not be dependent on the web container. It should be a J2EE standard complaint web app. In that case, it does not matter whether you use Tomcat or other servlet containers.
My situation is summed up in the "Configure JBoss/Jetty to use nsapi_redirect.so with SunOne 6.1" post.
The reason I am looking to upgrade Jetty is because there are issues with getting it configured to use a fronting web server via ajp13. I am unable to upgrade to a newer version of JBoss because of a third-party application that does not yet support newer versions of JBoss.
Nevermind, I figured it out.
To upgrade Jetty, simply replace the org.mortbay.jetty.jar file in the jbossweb.sar with the org.mortbay.jetty.jar file of the version of Jetty you want to upgrade to.