I'd go with Tomcat or Jetty if you only need JMS, and if you don't need an app-server managed transaction provider for transactions that span more than just JDBC (for example a transaction that spans JMS + JDBC).
While you can do JTA and JMS outside of an application server like JBoss, I've had very mixed experiences trying to get JTA to span JMS and JDBC under Tomcat. Maybe it was an early release of ActiveMQ, but it really ate up multiple months in a very important project. There is something to be said for the infrastructure that a J2EE server like JBoss provides, esp. when you do need JTA with XADataSources. Trying to recreate that with stand-alone components is confusing.
BTW, I'd consider Jetty over Tomcat if you have a choice.
As far as Tomcat and Eclipse integration, there are many options here. I use a (somewhat custom) plugin call Sysdeo Tomcat Plugin for Eclipse. The standard approach is to use something like WTP. I use the Sysdeo Tomcat plugin because it seems to have the lowest overhead. Another option is to just use the Jetty Eclipse plugin - again, I've found Jetty to be preferable to Tomcat in almost every way possible.