I had someone email me with the following question today:
I'm developing a ColdFusion app with Prototype. Seems Ajax.updater wants to insert my application.cfm code into my div along with responseText. How can I stop this?
This question brought up two good points. First the simple answer to his questions is that you can reset the output buffer using cfcontent:
<cfcontent reset="true">
The second point is that, for reasons like this it's not usually a good idea to output anything in Application.cfm or OnRequestEnd.cfm. It's better to just cfinclude a header and footer template.