Tomcat is not a full fledged Java EE application server, it is a servlet container. Therefore using Tomcat alone it is not possible to develop and deploy applications taking advantage of Java EE 5 APIs other than servlets, JSPs and JSF.
Although I haven't used any recent versions of Weblogic, at least in the past Weblogic had the tendency to try to trap you into their proprietary APIs, making the transition to other application servers difficult.
Also, GlassFish is free, support is available for about $4,000 a year, regardless of how many CPUs the server where it is deployed has (don't quote me on this, contact your friendly Sun sales representative for the actual price ), and Weblogic, last time I checked, cost about $50,000 per CPU (again, contact a BEA sales representative for an actual quote).
Author, <a href="http://www.packtpub.com/java-ee5-development-with-netbeans-6" target="_blank" rel="nofollow">Java EE 5 Development with NetBeans 6</a>