I relize this is a rather newbie question but I've seen stuff like this done before and seeing the Zelda model was really impressive.
Is there a site or some way to learn more about this process?
I have the Zelda models on my computer, plus I've also personally ripped models from Final Fantasy XII. I can use them in 3DS, but I don't know much about how to properly use them or apply them to programs like gmod.
I'd love to work on a way to get my own Balthier and Fran models into half life.

I've done some work with rigging, but nothing as good as what you've done.
Particularly on stuff such as clothing.
Any advice or links to help would be greatly appreciated.