You'll probably want the basic tool set released for JO by raven. There are several places you can download it from. Here's a link to the JKFiles download
ModView is a program included with the toolset, you can use it to view models already converted into .glm format, and is very useful for creating new skins for existing models. I have a tutorial on my site that can help those starting out with it.
For creating new models you'll probably want to check out a tutorial from one of the more experienced modelers. My personal Favorite is PsykOsith's tutorial.
.pk3's are the packed files that the game reads it's data from. They're similar to .zip files and can easily be read and created by winzip.