No, Flash and other plugins deal with mouse interaction on their own and cannot be interfered with from HTML. Even if you changed the wmode and layered other HTML elements on top of the Flash, having caught a click on an element you could not then route that click into Flash either.
So you can't catch a click on Flash unless the Flash is deliberately written co-operatively to pass information about clicks out to JavaScript (eg. by providing a listener interface). There is no way to reliably audit third-party Flash banner clicks.
About all you can do would be to listen for mouseover/mouseout on a block containing the Flash, and if the current window loses focus in between the mouse entering and leaving, make a guess that the user clicked the banner and popped up a new window. This is still massively unreliable (plenty of scope of false +ves and false -ves).