probably the best solution is the host that portion of the code on your own server and have the webmasters of these site include it into there page via Java.
That is probably the best way to achieve this.
I can't really see a way of doing what you want with accuracy. Because you never know how long it would take before someone actually clicked on the banner, and a time base system sounds like the only feasible solution.
You could also try looking into the possibilty of identifyers and store IP address of all the poeple who requested the Banner and then assign an id in a table that could be set to flag your clickthru.php script the id it needs to send them to the proper page, but if you expect this to get large that might get a little messy.
Just some thoughts though.