I spoke to a guy at ATMEL, and he instructed me on what I could remove. You can indeed just snip most stuff out, the dev kit just has everything there so you can try it all.
I realized though that the best thing to do is buy the dev kit and familiarize yourself with what you're using. Once you get one and start to understand how to program, etc, you can say "Yeah, I need this part, but not that one."
We actually put that design on hold and are going with a simpler processor for our first foray into the ARM world. Everything we have now runs off a PIC and is about 10 years old. It's aged pretty well but we'd like more power, so even a low end ARM looks good. I got a SAM3U dev kit and learned the basic, but then realized ATMEL is never going to actually *ship* a SAM3 part, so I've started designing based on a SAM7, and actually just brought up my first board yesterday. They're much, much simpler and a great intro to ARM chips, if you can use them.
And for my board, I mostly just copied the OLIMEX H256 schematic, which they have here:
http://www.olimex.com/dev/sam7-h256.html Its a barebones minimum part count board, just like what I had been looking for with the other processor. OLIMEX sells SAM9 boards too so they might be a good place to start.
I've also recently met some other people who might be able to help, but their time is not cheap, and I have no idea if they're even available. I'd just suggest going with an OLIMEX dev board to start, and then design your own based off that schematic.
-Taylor