<p>Ideally I'd like a way to enable the mouse wheel for scrolling in old compiled java runtime apps, but java code to explicitly utilise it for an individual app would suffice. </p>

Mousewheel scrolling is supported in current Swing applications. You could try compiling your application using JDK 1.4, 1.5 or 1.6. Depending on the complexity and environment moving to a new version may or may not be a viable option.
This tutorial
shows how to write your own mousewheel listener if you want something different to the normal behaviour.