The most recent build of HotkeyNet allows you to simulate mouseclicks in multiple windows. You can control the location of the clicks in various ways:

-- specify coordinates
-- duplicate the mouse's location relative to the foreground window in the other windows;
-- scale the mouse's location relative to the foreground window in the other windows, adjusted for the ratio of window sizes;
-- dupe or scale the mouse's location relative to the screen resolutions (HKN can be used on multiple pc's, so the screen resolutions can differ);
-- click at the mouse's current position;
-- etc.

The syntax looks like this:

<MouseClick Button Target Mode Restore>

With four parameters, there are a lot of ways to use this function, but each parameter has a default so the function can be very easy to use. If you simply write:

<MouseClick>

You get a left-click in the targeted window at a location in the new window which is the same as the current position in the foreground window, scaled for the difference in window sizes, if any. That sounds more complicated than it really is. I think this default is what most people will naturally want to do most of the time.

You can also control whether the clicks are delivered through SendInput or messages, whether the targeted window is brought to the foreground, etc.

More info about MouseClick here

Download HotkeyNet 48 here

This feature is brand new and hasn't been tested very much, so expect some bugs. Comments about the design of the syntax and suggestions for changes are always welcome.