Well, a lot of them that start with "Ant" use the Ant build system. If you don't know what that is, you probably won't be using it (although it's a good thing to learn and use). After that you have two choices for a Java Application and two choices for a Java Applet. Which you choose depends on what API you intend to use for the GUI. AWT uses heavyweight components native to the platform you're running on (like Frame), Swing uses lightweight pure Java components (like JFrame). Swing is the API of choice for most things nowadays, AWT was the original Java GUI model and AFAIK is rarely used today. Java Tool is for if you want to make a command-line (console) Java application with no user interface other than ASCII text, a backend data processing engine, or the like. A JNI (Java Native Interface) application lets you access platform-specific functionality, although at a loss of portability (although there are ways of doing JNI where other platforms can fall back on pure Java functionality). The Cocoa-Java application types let you use the Java language together with Apple's Cocoa APIs to give you direct access to Mac interface objects. I don't recommend going down this road since Objective-C is generally a much better way to use Cocoa and Apple no longer supports Cocoa-Java (although you can still use it).
Most likely you will be using one of these three, depending on what you want to do:
Java tool - text-based, command-line.
Java Swing Application - a double-clickable desktop application.
Java Swing Applet - a Java application that runs in a web browser (or Apple's Applet Viewer).
NOTE: It's been a few years since I've used Java, so someone please correct me if I'm wrong on something.
EDIT: I forgot to mention that there are other alternatives to using Xcode for Java on the Mac, such as NetBeans, Eclipse, JBuilder, IntelliJ IDEA, jEdit, SubEthaEdit, or the free TextWrangler. If you're doing simple projects in school I'd recommend staying away from the complexity of Xcode and try TextWrangler with Terminal for a bit.
