As the title suggests, this is in relation to Java EE and Glassfish in particular.
From what i've learned the application client is executed in some application client that has the ability to talk to glassfish. But there seems to be limitations to this regarding annotations.
Can someone give me an example of the difference in connecting to a glassfish application server from the two different application types?
What is the benefit of the application client approach, and what approach is the most commonly used when developing application clients for Java EE?
The code (work you need to do) associated with connecting to the app server in either case is not really all that hard... but it is covered in different docs.
These are the instructions on how to access an EJB from a stand-alone java application.
These are the instructions for using an app client to access an EJB from a Java EE 6 Application Client with GlassFish v3: http://docs.sun.com/app/docs/doc/820-7695/beakt?l=en&a=view
Accessing an EJB from an application client gives you access to more of Java EE services 'automagically' than if you were working with the EJB 'directly'. You can cobble together access to some of these services in the stand-alone case, but the burden shifts onto the application developer/deployer to make that access work.
Creating a stand-alone application that accesses an EJB will seem easy, in the short term, and many folks will invest in that strategy. If they deploy their client application onto a large number of machines, the burden associated with a cobbled together service access strategy can become a burden.
Deploying an application client that uses the application client container is not free either. The advantage is the fact that you have the support of your app server vendor to overcome deployment issues.
If you are using GlassFish (v2.1,v2.1.1 or v3), you can also take advantage of Java Web Start support, which simplifies client application deployment a lot.
An application client is actually run in a container and has full access to Java EE resources defined on your server in the same way that a Servlet or EJB does. This would typically be used for some type of admin client, not a user application. Here is one explanation.
In addition to the Java EE Application Client, there is also the concept of a Thin Client, which allows access to some Java EE resources as well, but not as easily as the App Client. It usually involves using JNDI lookup with absolute names as JNDI references are not available. A typical case for this would be a standalone producer/consumer of JMS messages. It is basically a lighter weight option of the full App Client.
If you are simply creating a user application, you will most likely want to either use a Thin Client model, or a plain old application that simply consumes services from your Java EE app via servlet or web service calls.