Frank Patrick says here that there are add-ons for Project that help model the uncertainty related to the number of spirals or iterations in a project. I have not looked at these add-ons but I'm sure that they do what he says they do.
He also says:
Although one aspect of the spiral is the unknown nature of how many times one goes around. That's what basic PM software does not handle so well.
My question is why should it 'handle' this up front? Sure you don't know how many times around the spiral you will go but you know you will go at least X times around. So you build your schedule around that number and then if you are pretty sure you will go around X+1 then you add that extra on the end. Then after you go a few times around you figure out that the real number will be more like X+3. So then you add those on to the end to make your model better.
Schedules are not deterministic so why should the model we build up front be anything more than our current best shot at the future?
Now that said I would love to see these add-ons and check out what they do to help this. But I do tend to concentrate on the core product. I have to since I cannot count on my customers using this add-on or that add-on. I CAN count on them using Project and Project Server. So I tend to try and find workarounds within that framework first before I look to 'custom' solutions. But I will take a look at some of these and try to report back on them with my thoughts.