UPDATE: This is old code using an early version of Atlas. Now that ASP.NET AJAX 1.0 is out, these samples are dead. Code is archived here just for reference.
Atlas and Prototype/Scriptaculous working together has been the subject of several forum threads, comments on blogs, and blog entries themselves.
The general consensus is that it just doesn't work, but I wanted to see for myself. I downloaded Scriptaculous and tried for myself. By just moving around some <script /> tags, I was able to get a Atlas + Scriptaculous demo running in about 30 minutes. I call it "Atlasculous," because I like inventing words by smashing other words together.
Disclaimer
Let me begin by saying that Atlas makes no guarantees that it will work in conjunction with other JavaScript libraries. Read this forum thread: Atlas causing javascript conflicts? for more information about why such guarantees aren't possible.
Further, the demo I wrote is very simplistic and doesn't exercise a whole lot of code from either Atlas or Scriptaculous. I have no idea if the two frameworks are generally interoperable, just that it's possible to get a basic page going. Even this functionality may break in the future, as it's an unsupported scenario.
Code
The only trick turned out to be changing the order of JavaScript includes. When I placed the Scriptaculous <script /> tags inside the <head /> like you typically would, it seems that the Atlas JavaScript (included from my <atlas:ScriptManager /> tag) clobbered something. I would get JavaScript errors when I tried to call Scriptaculous's Effect.BlindDown().
Simply moving the <script /> tags down below the <atlas:ScriptManager /> solved the problem. Look at the full code.
Download
Download: Default.aspx.
You'll also need Scriptaculous in the relative path "scriptaculous" next to Default.aspx.
Enjoy!