Making a mouse scroll work in non-active windows?

WizMouse will do the trick, and for free.

WizMouse is a mouse enhancement utility that makes your mouse wheel work on the window currently under the mouse pointer, instead of the currently focused window. This means you no longer have to click on a window before being able to scroll it with the mouse wheel. This is a far more comfortable and practical way to make use of the mouse wheel.

Try KatMouse:

The prime purpose of the KatMouse utility is to enhance the functionality of mice with a scroll wheel, offering "universal" scrolling: moving the mouse wheel will scroll the window directly beneath the mouse cursor (not the one with the keyboard focus, which is default on Windows). This is a major increase in the usefullness [sic] of the mouse wheel.

Another (optional) feature involves the wheel button. Since the wheel button is not consistently used in Windows, KatMouse can use it for a kind of task switching: with a click of the wheel button you can push a window to the buttom [sic] of the stack of windows that is your desktop, making a recovered window the active window.

KatMouse is free software.

For anyone looking for a free alternative to the ones already mentioned, Taekwindow is worth checking out. Besides the brilliant name, it offers some extra functionality that you might deem important:

• move a window by grabbing it anywhere (not just the title bar) while holding the Alt key, and then dragging with the left mouse button;
• resize a window by grabbing it anywhere (not just the tiny little border) while holding the Alt key, and then dragging with the right mouse button;
• move a maximized window between monitors by Alt-dragging;
• use the scroll wheel on the window under the cursor, instead of the currently focused window;
• push a window to the background by middle-clicking on its title bar.

You can quickly enable/disable the program by left-clicking on its icon in the systray. Personally, I found it one of the most lightweight apps that offers the requested scroll-under-mousepointer functionality, as well as one of the most stable. It's a minuscule download (28K) and doesn't require installation.

I'm not affiliated.