I just answered this on the AZ CFUG (cause, they actually TALK over there, lol)... and I thought I'd share:

Question:
The problem is if more than one change for intranet needs to be tested at the same time on qa, we can only do this one at a time since we only run one instance of CF (intranet) on QA. If one change gets deployed to qa that would override the other changes that were previously being tested.
Has anyone else ever had any experience with this type of situation?

My Thoughts:
Use the application.cfms CurrentTemplatePath to establish the appRoot for this application.
Use the difference between CGI.PATH_INFO and appRoot to establish the true webRoot.
Use CGI.HTTP_HOST to ID your server and decide if its applicationClass is Dev, QA, or Prod, which you can use to control elements like whether or not to allow certain overrides or what databases you use.
I generally set a serverName variable at this same time, rather than using CGI.HTTP_HOST because you DON'T want the application differentiating between DNS variations that all point to the same application (like www.widgets.com, getwidgets.com, widgets, and 68.87.123.12 or whatever potential naming options you have).

Name the application based on the appRoot ( ie, name="widgetyzer_#appRoot#" [or potentially name="widgetizer_#serverName#_#appRoot#" if your Dev/QA/Prod share databases]), so it doesn't dance on anyone else's vars.

It also allows you to move things like Image, css, and script folders to the webRoot... so you don't have instanced code trees full of extraneous crap.

Now you know what your server is, what its purpose is, and have a distinct application framework for each folder... you can move folders around, and drastically alter code, without worrying as much about code conflicts and whatnot.

Anyone else have thoughts or a different or better methodology?