I am using Tomcat for hosting my Java Web and Web Service applications for a long time now. Mostly for Spring and Grails appli
I would go for Optional Packages: http://docs.oracle.com/javase/6/docs/technotes/guides/extensions/index.html
Steps:
Package your code, libraries in a jar/war.
In the MANIFEST.MF of the above declare the extension list jars
Referred them in the target applications