I have been doing some tinkering on this.

I wrote some perl code to take fare routing rules and come up with all possible routes. (Hopefully. UA's routing rules are so many lines long, but by using the timetable to trim down bogus routings it seems to process in reasonable time.) Then I have code that sorts those routes by distance and finally it looks through the timetable (using the published pdf timetable which I parse in) to find which routes one can actually fly. (Would be fun to play around with interesting constraints like equipment type, etc.)

Still it has got some issues though. But if there is interest I will keep working on it. I noticed it seems that AA uses an almost identical timetable format, so maybe the code won't have to be limited to UA but could also be expanded to the dAArkside.

One hang-up is that I am not sure where routing rules for fares can be found anymore. Farecompare, as mentioned by others is a great starting point for find good fares. I wanted to simply be able to go one step further once I had a specific fare and route in mind, to find the best flights. Eventually having those flights, it is a piece of cake to have ITA check availability using another script (to generate the ITA syntax to find those exact flights, etc.) which I toyed around with.

Sorry if this message is a bit incoherent or poorly written. I have a really bad head flu right now. It made my 5 segment transcon flight rather miserable.