www.nonrev.net

That is the best one I have come across yet. It will bring up connections with one carrier on one leg and a different carrier on another.

i.e. United to ORD and AA out of ORD to your destination.

Where as passrider.com will not as far as I can tell.

www.nonrev.net also has Airtran's flight schedule included as well. I still haven't found one with Southwest schedule included.