What is a good design for a Capstone Course in CS?
Personally, I'm a believer in a project based capstone and a group one at that.

The project should involve going from generating (and pitching) an idea through design, development and ultimately delivery and should require integrating multiple tools. 

Since many kids would want to use such a course as preparation for internships and jobs, I'd say it's more appropriate to take in the junior rather than senior year. That's ok though since you're done with most if not all core major requirements by then and are taking electives.

I know taking a capstone prior to the senior year sounds wrong to some but it should show mastery of many if not all of the core concepts in a typical CS major and fill a big hole in a students development.