How do you compensate for templates, template plugins (I use Template Toolkit (Template)), application modules, instance scripts (I use CGI::Application) and non-application modules being inter-dependant?

Templates are part of the web application and get checked in (and I use Template Toolkit as well). Likewise, template plug-ins and instance scripts get checked in.

The 'non-application modules' are part of a system installation that we track using Red Hat RPMs. That's not easy, but I work with the SysAdmin and we keep that system in check.

How do you write tests that depend on your webserver config (and its environment) and package them with your module?

Because we used a kind of Rapid Application Development approach without tests, we don't have any automated tests for the web application. Yes, I wish we did, and I hope to be able to use WWW:Mechanize to address that in the future.

How to you get your personal machine to emulate the environment of multiple machines?

I don't -- I use a combination of my development system and my test system to develop and test new versions of the web application.

How do you move material to your test server, and from there to production server?

I wrote an installer for the web application that's part of the checked in source. I extract a specific revision from the source control system, run the installer, answer a few questions, do a very small number of tweaks (they're on the ToDo list for the installer) and the system is ready for a smoke test (if this is for a Production system).

Once the smoke test passes, the system is passed on to the customer rep, who passes it on to the customer.

How do you do some of these things in a multi-user environment? (Is the test server a "check out"? Who checks it out?)

I'm not sure I understand your question; I'm the only developer for the web application, so I don't have to negotiate with anyone for a common file that we both want to work on. I can check files out of the source control system onto the test system for development, just because it's a more capable system than my own workstation for some configurations. That's not a big deal.

Hope that answers some of your questions.