I came across an interesting blog posting about the Prototype Javascript package and how it compares with Atlas. It boils down to they try to do similiar things, but come from different directions. Atlas is server-side centric and is designed to bolt into Visual Studio and Prototype is client-side oriented and isn’t a .NET tool (100% Javascript). Check out the links to moo.fx and Rico in that article, they are doing some cool UI things with Prototype.