Hey, congrats,
Like quietriot said, basically the changes from 2005 to 2006 are the stereo system. You can no longer get the multi-disk changer but you have the option for getting the iPod stereo instead. Also, the steering wheel on the 06 has stereo controls.
There are two new colors which replaced 2 old ones on the 06.
Oh, I have the Yokohama S32A tires on my 06 rather than the Potenza on the 05.
I can't think of anything elses.
One thing I want to add is that with the SCION, you are probably not gonna see the car you want on the lot. You'll probably have to tell the dealer the color (and options) you want and place a deposit to hold the car.
I bought mine from Carmax in MD. I first talked to my salesperson via e-mail telling him that I wanted (actually my wife) Azure Pearl with side air bags. He told me that he would contact me if a car with such options come in. When it did, I mailed him a deposit for $500 and he held the car for me until I was able to go in and do the paperwork.
I added more options to the car and when it was done picked it up.
So, it's quite common that you won't see the color you want on the lot, you'll just have to be patient about it.
Unless it's too late, you may reconsider and wait for what you really want since you'll probably feel much better about the purchase later on.