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What is the "usual way" to create a GUI for your application?

Hey guys I'm new to programing and I'm just gettin into UI design.
There are some things I've gotten so far, like I should only use a JFrame per application and other guidelines like that. What I don't understand is... what is the proper way to join your business logic with the GUI?
What I mean is, let's pretend I've just created an application that runs on console (or whatever), and I want to create a GUI for it, so, I've seen on the net that people create a JForm-derived class as a main class and that's it. But is this the proper way? I would like to keep my original "Main class" (the class that uses every other class I've created for my project) and define the form as a field of it, something like that.
Is it possible? If so, how can I achieve this? I have all my logic on that main class I just talked you about, so when I instantiate the form inside of it, I don't know how to make the form use and alter the fields and use the methods I defined in the main class (Sorry if I'm not making myself clear).
How you do, experienced people, do it? What is the "good practice" way? Thanks for taking your time and sorry if it's a noob question.

I'm no professional but I can't stand working with JFrames and Graphics objects.
Most of the time I use the lwjgl library. I know this library is for games but It is
great for UI's as well. The reason it is so easy is because you simply give buttons their
X and Y coordinates without having to worry about layouts. You can make your own images and
import them easily, so if you want your button to look like an image you created no problem.
Because it is made for games it is also very fast and fluid.
This may not be the best way but it works for me so I thought I would share anyway.
Hope it helps.
Here is the lwjgl website: http://www.lwjgl.org/
Here is a video series that helped get me started: http://www.youtube.com/watch?v=0v56I5UWrYY&feature=c4-overview-vl&list=PL19F2453814E0E315

Paranaix already mentioned in his comment about the model - view - controller architecture.
I mostly construct Java Swing GUI applications.
I build the model first. This could be considered a "first cut", since I update the model as I construct the view.
Next I build the view. I construct all of my Swing components by hand. I find that GUI builders harm more than they help. Building the view usually causes me to modify the model.
Finally I construct the controller.
Here's a more detailed description of how I put together a dice game from my blog.

Java - Structuring the flow of data in GUI from input to output

I'm putting together a GUI with a couple of panels.
In one panel there are components for the user to input various parameters.
In another panel, there are buttons and a place to output a plot based on data
generated using the user inputs.
I have all of the various pieces working independently now I'd just like them to
talk to each other!!
When i hit one button, I would like to take all of user inputs and combine them to
generate a data set and plot it.
Another button then to write this same data to a file.
I have code to implement all the components individually, code to write data to
a file and code to generate a plot from data. All of which works fine.
I thought that I could use the Action/ChangeEvents to take the parameters and
assign them to an ArrayList. Then use this arraylist to generate the data.
I'm finding it difficult to plan an approach to tackling this.
Currently I'm using get set methods in the event handlers to set parameter levels for
a particular instance of the array list, I would like to pass this instance into another class to generate the data but don't know how to make it accessible.
I hope I have provided enought information here. If anyone has any
thoughts on this they would be much appreciated.

I think a structured way to tackle your issue is to apply the MVC pattern. Here is what I think a seminal article about Model-View-Controller (MVC) using Java.
Java SE Application Design With MVC by Robert Eckstein,
and here is another sample code.
As for taking the parameters from one panel and pass them on to the other panel, you can use the Command Pattern. What the pattern does is basically encapsulate all the information needed for a method to perform (an instance of a class, parameters, etc.) into one Command. This Command then can be passed around in the application, simplifying the way you execute the method.
A good book about Design Patterns, by the way, that I really love is Head First Design Pattern.
EDIT:
I'd just like to add some links discussing about MVC and some other GUI architectures that I find useful:
GUI Architectures by Martin Fowler
Build your own Composite Application Block series: UI Architechtures, Patterns and WinForm Examples
MVVM vs MVP vs MVC: The differences

This seems like a good case of application of MVC pattern:
http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller
Another good resource would be this book's second chapter:
http://www.amazon.com/Design-Patterns-Elements-Reusable-Object-Oriented/dp/0201633612/ref=sr_1_1?ie=UTF8&qid=1334437965&sr=8-1

java - Best way to display object properties

Reflection or hashmaps? Suppose you are writting a graphical application where you have objects lying around and users have the posibility of clicking on them. That said, you want to display the clicked object information somehow.
I end up reading Accessible interface from accessibility java package and AccessibleContext class... Before that, I wrote testing code using hash maps for properties instead of class fields. And lastly, I thought in Reflection after reading that JavaBeans use instrospection.
What would you recommend in such applications?

Using reflection and introspection sounds like a better approach than using HashMaps. Instead of using this API directly, I would recommend an abstraction layer like Commons BeanUtils, which will allow you to work with classes adhering to the JavaBean standard in an easy manner.
Here's the User Guide complete with examples.

I want to change the language of a SWT Application at Runtime. How to do that?

I'm developing an application to my software engineering class and one of the requisites is that it has 2 or more languages in the interface. I already implemented that. On the other hand, it is required that the user can change the language on its own will by choosing from a combobox or something like that.
As i'm using AWT and Netbeans, I can't edit the initComponents method of the form, as it is automatically generated. I have the option below in mind, but don't know if they would even work, so I'm asking for help.
-Edit the constructor of my class so that it looks like this:
public JFmyConstructor() {
initComponents(); //auto-generated
myInitMethod();
}
The problem I think i'm going to find is that I need to call the constructor one time after the interface is already running (and thus, all objects instantiated. Is there a workaround for this?

Probably my answer comes a little late (too bad you put wrong title)...
Obviously you do not have to call any constructor in order to switch language at runtime. In Java Desktop applications it is as ease as:
Locale brazilian = new Locale("pt", "BR");
Locale.setDefault(brazilian);
Of course if you want to switch it via JComboBox, you would probably do it a bit different. What I would do, I would actually create Model (Swing promotes MVC Design Pattern) that will hold data (different Locales) and I would set default Locale in correct ActionListener. It is not easy though.
Of course I would rather use native names for Locales. If you have them constructed, you can easily get native name Locale name by simply calling getDisplayName() passing itself as a parameter:
String brazilianNativeName = brazilian.getDisplayName(brazilian);
The result might be unsatisfactory for certain Locales (I believe Brazilian Portuguese is unfortunately one of them), but there is not much you can do about it (unless you use your own string).
To be honest, for just two languages, I would probably use some links instead. You can use simple JLabels to do that, just set correct font properties and color and assign common ActionListener. You can then query which one was actually clicked and create and set Locale appropriately. For homework that should be sufficient.

SWT and NetBeans is a weird combination. If you can do things the "normal" way with SWT and use Eclipse, then there's a powerful set of tools for managing localization, all built right in. See, for example, this introduction.

The best way is to use resource injection for all components (rather than getting i18n strings from a Bundle at panel construction time).
Resource Injection is available in a number of open source libraries or frameworks.
Since you use NetBeans, you should be able to generate an application based on Swing Application Framework (SAF), which already supports Resource Injection.
Otherwise, there are also libraries out there that do just that; simply google for "swing" "resource injection" and you'll find, e.g. Fuse library.
Edit:
You should also take a look at this SO question that deals exactly with the same problem, and which has more detailed answers (including my own).

What component should I use to draw a dendrogram in Java?

Dendrogram is not a regular diagram. Should I use any component from javax.swing.* library, or just draw it with java.awt.Graphics?

Might also be worth checking: yWorks and JGraph

I don't think there is a standard component for this. Unless some component vendor has done one, you should go the Java 2D way...
If you don't want to do the hard work, perhaps one of the above mentioned libraries might help you. Otherwise, GraphViz is good at making this kind of diagram, and has a Java API (untested...).
Another possible way is to use some physics to let the nodes arrange themselves in an harmonious way. That's how Aharef's HTML graph works...

Netbeans Graphing API
By far the easiest and most intuitive API of the lot.