<p>Whats the best practice for setting up package structures in a Java Web Application?</p>

<p>How would you setup your src, unit test code, etc?</p>

You could follow maven's
standard project layout
. You don't have to actually use maven, but it would make the transition easier in the future (if necessary). Plus, other developers will be used to seeing that layout, since many open source projects are layed out this way,