Some quick 'n dirty testing guidelines:

• It's easier to test modules than scripts. Move the code to be tested into modules.
• It's usually poor design to have a function or method do too many things. Coincidentally, it makes them harder to test. Break them into separate functions.
• For scripts, I frequently have a DEBUGGING constant. If it's true, I have it runs tests embedded directly in the code (it's easier if you can run the CGI script from the command line). You can see a simple example of embedding tests (without the constant) at Why is goto &sub slow?.
• You can also mock up troublesome interfaces (if they're tested separately!) by using Test::MockObject or something similar (I frequently localize the sub and have it return results directly).

You might also be interested in Test::AtRuntime. It's a great module that can solve some of these problems.