I've used several spreadsheets from the AISC website as well as from Alex Tomanovich concerning crane runway systems. I receive numerous requests (perhaps dozens) each year where a customer wants us to analyze a crane runway system where multiple cranes may be operating in the same bay at the same time. This occurs frequently when a customer investigates purchasing an existing building with an existing crane runway system, but wants to modify it to meet their specific needs. Also, the runway girder options should include S, W, S with channel cap, and W with channel cap combinations. I think the program on the AISC website is the closest program and perhaps could be modified to meet these needs in one comprehensive program. Does anyone have any thoughts on this subject?

I am not sure what code of practise you use but if the analysis is linear elastic analysis then theory of superposition will apply. In this case you can add the results of one loadcase to another.
You could use Alex's BEAMANAL.xls and move the loads across the crane runway. You'll need to introduce a few calculations to generate the load tables from the position of cranes but this should be pretty straight forward.
Once you have set this up you can use XLC's animator button to move loads across the runway and watch SF or BM diagrams change as the load moves. Alternatively you could link each crane position to scrollbars to control which will provide a nice interactive tool. I have use this for simulation of an excavator arm and it worked quite well. Excel's goalseek or solver functions will be very useful to calculate positions of maximum bending moment in the crane runway.
Is this the kind of thing you are looking to do?

What is the question regarding? The thickness of flanges subject to wheel loading, the sizing of the runway beam, is it a monorail crane or bridge beam crane, or is the critical issue the influence of the cranes on a building structure supporting the runway? Also what is the bay referred to: spacing between frames, or adjacent multi-span frames?

For the building frame the maximum axial load on the columns would be when the two or more cranes are operating as close as possible to the column. How close they can get is dependent on their wheel centres. It also depends on any proximity limit switches which may be installed on the cranes preventing them from operating too close to one another.

As John says use superposition. Assess the influence of one crane, then the influence of others, then assess whether the two cranes can be in the locations which generate their maximum effect at the same time.

If you are bumpering 2 bridge cranes together, as long as you don't have more that 8 total wheels for the 2 end trucks on one side, then you can make use of my "MOVLOADS.xls" spreadsheet workbook. It will determine the maximum moment and deflection for the crane girder, as well the maximum reaction at a crane column for 2 adjacent spans.

Alex