The new oneworld interactive network map does something similar to what you want I think:

http://www.innovata-llc.com/onw/default.asp?show=MAP

Click on a city (for example Madrid) and it will show lines to all the direct destinations from that airport. Then click on a destination (like Miami), then click on "list direct flights from Madrid to here" and it opens a window with the airlines that serve that route (in this case AA, IB). Then click on "View timetable for all flights" and it will list all options between those cities.

Far from perfect, but not bad.