There are many good 'stacks' that you could use, some of which have already been mentioned.
They all have their own strengths & weaknesses, and you really need to select a stack that best fits your requirements.
The Spring/Roo, AppFuse & Seam are all great, but they do come with a certain amount of... errm... bloat.
You may find that picking and mixing technologies actually provides you with a lighter weight and more performant solution, so long as the technologies you choose integrate relatively seamlessly.
If you're looking to package a full execution environment including the servlet engine as part of your application, Jetty is a good choice, and you can easily integrate it into a Maven build environment.
You may also want to investigate using HyperSQL for your database, which will allow you to prototype using an SQL compliant database without having to worry about installing a full database manager such as MySQL or PostgreSQL.