I think this is what you are looking for:
http://www.flightlookup.com/index.html
This is the on-line version of
Electronic Travel Desk timetable from Goldenware Software. I use the downloadable version on my PC so I can use it off-line (it has even more functionality, about 20mb), but this is an on-line version. It will give duration for connections as well as direct flights, and you can even sort by duration.