Clark wrote, "I assume some applications don't work as well as others in a virtualized environment. Is there a list?"
Great question, Clark. Applications and software that are tightly linked to the operating system, such as system drivers, OS patches, and Internet Explorer, and server-based applications such as Microsoft SQL Server and Apache are not officially supported in SVS 2.0.
However, you'll want to frequently visit this Wiki article that shows users' experiences with both supported and unsupported applications virtualized with Altiris SVS.