I haven't played Quake 3 recently but here's how I set it up in Mouseware (since I haven't played I'm not 100% sure it will work but it should so just try it)
Set the middle button to 'Autoscroll'
Once you did that click on the Options button with the asterisk that is under the picture of the mouse.
Goto the 'Autoscroll' tab and enable 'Use ms compatible scroll only (works as middle button)'.
Make sure under the scroller part of the 'Buttons' tab in mouseware
that 'Use ms compatible scroll only' is disabled.
I think this is how to set it up so you can scroll in windows with the wheel (without needing to press a button), use mouse3 in games, and use the wheel to scroll weapons or whatever in games.
eagle