<p>We use Tomcat to host our WAR based applications.  We are servlet container compliant J2EE applications with the exception of org.apache.catalina.authenticator.SingleSignOn.</p>

<p>We are being asked to move to a commercial Java EE application server.</p>

<ol>
<li>The first downside to changing that
I see is the cost.  No matter what
the charges for the application
server, Tomcat is free.</li>
<li>Second is the complexity.  We don't
use either EJB nor EAR features (of
course not, we can't), and have not missed them.</li>
</ol>

<p>What then are the benefits I'm not seeing?</p>

<p>What are the drawbacks that I haven't mentioned?</p>

<hr>

<p>Mentioned were...</p>

<ol>
<li>JTA - Java Transaction API - We
control transaction via database
stored procedures.</li>
<li>JPA - Java Persistence API - We use
JDBC and again stored procedures to
persist.</li>
<li>JMS - Java Message Service - We use
XML over HTTP for messaging.</li>
</ol>

<p>This is good, please more!</p>

Cost isn't necessarily a downside as there a few free J2EE servers, e.g. JBoss and Glassfish.
Your question assumes that (J2EE = Servlet + EJB + EAR) and therefore, there's no point in using anything more than a Servlet container if you're not using EJB or EAR. This is simply not the case, J2EE includes a lot more than this. Examples include:
JTA - Java transaction API
JPA - Java persistence API
JMS - Java messaging specification
JSF - technology for constructing user interfaces out of components
Cheers,
Donal