Many people have asked what programs I use to make the animation on the site. Here is an overview of the software involved, as well as books and manuals that I have used. I am not going to assume any prior knowledge on the reader's part, so the more experienced may want to skip forward a little.

Firstly, the animation on the site is in the format called "flash". A company called Macromedia makes two Flash programs:
the Flash Player that plays the files in your browser (which is free) and the Flash program that generates the files (which is not). When I refer to Flash from here on, I am referring to the full version of the software, not the player. For more info on the Flash Player check here.

I make the animation for the site using the Flash 4 program. The program has recently been updated to version 5...however I don't like it very much, and will be sticking with version 4 for as long as possible. Version 5 has a very clumsy gui, and seems to be buggy. If I were you I'd try to get a hold of version 4. The price is high: Flash 4 sold for somewhere around $3-400, Flash 5 is similarly priced. If you are a student or on a low budget, it might be worth looking for a student version. Someone told me that there is/was an educational package of Macromedia software (including Flash) that was a little over $100.

With Flash you can import photos or line art that you have scanned, place them anywhere you want, animate, resize , rotate, tint, or make them transparent. You can have as many layers of video and audio as you want. It's a pretty flexible program, and it's not that difficult to learn, if you're doing basic stuff. (If you want to do more interactive content then the learning curve gets a bit steeper. Moving images around the screen isn't too tough!)

The key to being productive with any software is a decent manual. Most programs these days don't come with very good documentation, so you have to find it on your own. Nothing is more frustrating than a slipshod manual. Here is a list of good computer manuals that I have used.

I use other software to make the animation. You need some kind of sound editing software for your audio work. I use Soundforge. It's straightforward and self explanatory...it doesn't take long to get basic sound work done with it.

Photoshop is handy for image manipulation, resizing, reformatting, etc. You may have simpler and cheaper alternatives; it's the one I use most, that's why I mention it here. There are lots of simpler and cheaper alternatives.
A free alternative is GIMP, an image processor that began it's life on Unix/Linux machines. There is now a version for both Windows and MacOS X! I haven't used GIMP myself first hand; I'm just giving you the option. Dreamweaver from Macromedia (the makers of Flash) is the web design program that we use to build the site. It's got quirks, but it's a lot better than some other apps that I could mention.