The lobster and uni mousse is a must have, as is the uni wrapped in squid. I second the rec on the geoduck dish and the fluke preparations have always been stellar. I also love the steamed sea bream.
I've had two of my favorite meals ever at Soto. It can get pricey though, especially when you tell them to give you anything so long as it has uni.
Here's the photos from my meal there last year: http://www.flickr.com/photos/lawandfo...
Yeah, he's a master of uni for sure - he understands and exploits the subtle differences between Atlantic and Pacific varieties. Standouts are the Miso Soup - which has a lobster & uni broth, the Uni Ika Sugomori - uni wrapped in squid with quail egg, and the Lobster w/ Uni Mousse, which has smoked(!) uni.
There are many other great dishes as well, but I'd definitely get a few uni dishes as part of your meal. I'm fond of what he does with clams - the Hokki Nuta (clams with miso-mustard sauce) and Geoduck salad are both great. My standard meal (for two) there would be two or three uni dishes, a couple raw dishes, and a couple kitchen dishes. Usually skip a sushi / sashimi course - they're good, even great, but the excitement at Soto is over the prepared items.