I would base it on the smaller the ribbon the less cumbersome it is to use. A 0.05" ribbon cable for 50 wires is about the size of an IDE hard drive ribbon.
Edit:
Did some checking based on images, its quite clearly using 0.025" or 0.635mm pitch ribbon wire between the scope and pods. Nice and standard, and also reduces the amount of connectors it could be.
So for each pod of 8 channels, there is (ground, 4v, +2.5, -2.5, Vref, 8 differential pairs) at minimum 21 signals, do we want to make these devices purely compatible with what is already in place, or make it designed around 2 seperate 8 channel pods? e.g. have a little breakout board at the scope end to 2 plugs for the pods?
I was thinking something like the Hirose ST40 series connectors, most likely the 24 pin one, but as they don't have prefab cables, Its probably not a good option for a projec tlike this. the scope end is 0.1" 2x25, shall we just make both ends the same? or do we get creative with smaller ribbons or more flexible wiring? by using a little adaptop board that plugs in at the scope?