For CGI apps, I suggest you start by looking at
CGI::Application. It's simple, light-weight and gives you a fairly good structure for building your own apps on top of it.
In general, you want to structure your modules so that related code is in the same, or related modules, and unrelated code is separated into other modules. For instance, you may want to have "generic" HTML generating / templating code in one module, and have database-access code in another. Once you do that, you should also take a look at CPAN, since there are many many modules there that help you with these subproblems.
Also see this article I wrote on MVC for the web - at least as a short introduction to a common way of separating concerns in web apps.
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