We were at the parks in 2002 and 2003 during marathon time. I can't say that I noticed any real effect on the crowds - parks generally seemed as thinly populated as they usually are that time of year. The day of the marathon can cause some traffic congestion in terms of getting around among the parks, but it's manageable and very temporary. The marathon does run through each park, I think - at least we encountered it at the Animal Kingdom. Again, it wasn't that the park was particularly crowded, but it affected traffic patterns because the CM's try to keep guests from getting in the way of the runners who are running on the paths. CM's hold guests back from crossing certain paths until there is a break among the runners. But it doesn't take long for the majority of runners to get through a park, then things get back to normal pretty quickly. It's actually fun to stand for a few minutes and cheer the runners as they pass - they really seem to appreciate it.