We were at WDW in 2002 and 2003 for Thursday-Saturday of Marathon Week. It didn't seem to affect crowd levels in the parks much at all - attendance was still very low and waits were very short or non-existent for most rides. The day of the marathon itself (Saturday)is a different story. The race winds through each park, and it does create some congestion as it goes through each park, mostly because the CM's redirect or hold back foot traffic so that the runners can pass unhindered. But it doesn't take long for the majority of the runners to clear out of each park, and then things get back to normal very quickly. There will be some traffic congestion, again due to re-routing for the race - on Saturday mornings that can affect you if you're driving or taking a bus from park to park, but again, that mostly clears out by early afternoon. It's basically not much of an issue.
