I've been doing this stuff for a long time. The technologies have progressed quite a bit over the years. If I had to start over today, these are the tools I'd choose:
App server: Resin 4
Web frameworks: RESTEasy, htmleasy and JSR299 (as part of Resin 4).
Persistence: Hibernate with ehcache for the second level / query cache.
Database: MySQL and Sequel Pro is awesome (try the nightly builds).
Presentation layer: Mix of JSP/JSTL with GWT controlling the forms and complex widgets. json and gwt async rpc for communicating with the backend.
IDE: Still sticking with Eclipse cause it is free and works well enough.
Other interesting technologies: HornetQ for messaging. Infinispan for data grid and possible map/reduce framework in the future.
I've recently spent some time with Stripes and I like it a lot, but the resteasy / htmleasy / jsr299 combo is so much more powerful and complete (while maintaing a fairly simple api), I just don't see the point in using Stripes.