Organizing packages is a matter of taste. Sun recommends the reversed DNS model for packages, but I find it's not strictly necessary, and projects like Akka and Play are starting to break with that tradition (they have top-level namespaces of akka.* and play.* respectively). If you do go that route, you obviously don't want to use a really generic word as your top level package like game.* for instance. Using your project name is a good idea.
As for organizing sources, I'm a fan of using the maven layout, even if I'm not actually using maven.
A typical maven layout looks like this:
It looks a little deeply nested but any IDE should give you a package view that hides all that. It makes it easy to support multiple languages (only compiling one language at a time) and easy to find resources like assets and config when they're not mixed into the sources. Compilation goes to a target/ directory, and the internal organization of that isn't all that important as long as it works and that you're able to blow it away any time you want.
Version control is just plain mandatory. Not using version control is like never saving your documents. You should get in the habit of thinking of your filesystem as just a local cache, where you're really saving your files to VC. As preferred version control goes, I would recommend something decentralized like git or mercurial, but even subversion is better than nothing.