I need to run on my development Linux server an instance of Tomcat v6.0 so I can test the apps I develop. On the same (physical) server, I need to run an instance of hudson-ci. Since Tomcat will be on and off more often than not, I consider running another server (i.e. JBoss AS 6) on a different port for the continuous integration software.
Is there any pitfalls I should be mindful of ahead of time?
No, just make sure there are no port conflicts (each one will use multiple ports). You should be able to start Tomcat, and then start JBoss, look for errors, fix, repeat.