Can somebody tell me the advantages/disadvantages of Allaire JRun versus Apache Tomcat?

JRun is a J2EE compatible container. For this reason it supports (besides JSPs and Servlet) EJB as well. JRun is actually a plugin on a web server in order to redirect JSP and servlet calls from the web server (propably non java enable i.e IIS) into is's WEB container.

Tomcat is a plugin itself but implements only the WEB container (i.e it can run only JSPs and Servlets -no EJB o JTS or other APIs of J2EE)