Ours look like this:
web/
web/WEB-INF/ (sometimes we use a conf/ dir at the top level but this is minimal)
src/
lib/
The build.xml has three targets:
- jsp: copies everything from web/ into the tomcat webapp folder and from lib/ into WEB-INF/lib
- compile: compiles everything from src/ into WEB-INF/classes in the webapp
- war: runs compile, jsp, and then zips the contents of the tomcat webapp into a warfile
This structure is a little bit informal and you can do it more cleanly by having a separate build directory for the warfile, and/or a separate compile directory, etc. Some people don't like the idea of deploying directly to the webapp instead of building a war first. But to get something up and running quickly, the above will do nicely.