Virtual Plant

Which package shall I download?...

...You ask. And, for there are four packages for this project, your doubt is nothing but fair.
The four avaiable packages contains files for the current version, v2.6.22r03, and the only difference between packages is how deep you want to go into this project.
Here is a short explanation on the contents of each package, given that all of they come with README.txt and LICENSE.txt files:

Jar-Only Package

Package = Jar Binary + Execution Scripts

This package contains the jar binary along with two convenience scripts for easily running the game.
This one is ideal for the one who want to download very few data, and it contains everything needed to run the game.

Source Package

Package = Source code

This package contains only the source code, as .java files, if you want to see, study or alter it, accordingly to the license, of course.
This is for those who want to se what's behind the courtain of binary execution: programmers, curious people and so on.
Note: There is no compiled files in this package, so you must compile the project by yourself in order to run it. I recommend NetBeans to those willing to venture into the java world (and even for other languages).

Javadoc Package

Package = Documentation

This package contains only the javadoc (the documentation of this project), the same one available in the site here.
The documentation is of interest to the ones seeing the source code.
Note: Again there's no binary file, requiring compilation in order to run the application.

Full Package

Package = Documentation + Source code + Jar binary + Scripts

The complete package, containing everything the ones above does.
Aimed for people who want the binary pre-compiled and still want to see the code and documentation.