Just to be sure that I write this up the other basic part of my project methodology is unit testing. Each set of tests I run are run on the same day, one after the other. Exact replicas (in terms of HTML output) are being compared and the code behind is as similar as possible.
Unit testing implies targeting a small subsection of a system and testing it alone. I am carrying out unit testing because if I weren’t doing that it would be impossible to separate the result sets. It is assumed to treat each page of a website as being completely independent of all other pages. In reality the pages could in fact be executed each on a separate server so this should be a valid assumption.
Sometimes it will be necessary to draw inferences between batches of unit tests. When this is done I do some simple, undocumented testing to ensure the results of the older test still ring true. There should be no significant difference because my server configuration is static and my systems are isolated from external networks.