Geogebra Download
This is a really great program that I use a lot to create my mathematical models. It is not necessary to have it for the class but you might enjoy it. There is manual on the website and a strong international user forum to help you get started with it. And best of all it's totally free!
Phun
This is a 2-dimensional "physics sandbox". You can use it to create physical models and it is amazing what some people have built on it (check out the phunbox). It isn't necessary to have it for class but I thought you might want to know where I get some of the computer models you are seeing in class.
It's a pretty thorough and versatile program and it's free!! (for now)
Java
You need to download this for most of the web links to work. You don't have to add the google toolbar unless you want to.
Flash
If you don't have this, I wonder if you even go to the internet. It's used a lot for web based media.