The huge difference here (obviously) is focal length and Image Stabilization, both of which play into how to pick which lens will work best for you.
If you plan on photographing subjects that would benefit from a greater working distance (insects, animals, etc) or lighting is an issue such that being further back helps, then the 180L obviously has a huge advantage here. If, however, that isn't a relevant issue for you then it can actually be a PITA to have to be ~2x further away from your subject to get the same frame, this was my experience with it at least.
The other thing to consider is with ~2x the focal length camera shake becomes a greater issue, you pretty much have to work on a sturdy tripod with the 180L but with the 100L you can get away with hand holding or less sturdy supports, adding IS to that equation helps the 100L even more.
You could also throw focal compression into consideration but the other issues seem more pressing. Also consider what else you could use these focal lengths for, I find I have several lenses in the ~100mm area but only 1 (70-200) that gets into the ~200mm range.