I think the WDW marathon is the following weekend. I heard this year was slightly more crowded than people thought it would be. But they said planning is the key, don't try to just wing it.
We were there one year right after New Year's. I think we arrived on the 3rd and I thought the crowds were not bad at all. Not sure about the marathon though, or if we were there when that was going on. We had fun at that time because all of the Christmas decorations were still up and we seemed to be able to extend our Christmas spirit for a little while longer than usual!
The Marathon is always the weekend after New Year's, but the crowds are barely noticeable. The only impact the Marathon makes is it can slightly disrupt Disney bus service on Saturday and Sunday (Jan 6 and 7 in 2007).
We arrived January 1st of this year, and found most of the week to be VERY crowded! Of all the times we've gone to WDW, that week was the most crowded of any we've been. I expect the same for next year, especially since New Years Day falls on a Monday.
We go to Disney quite often right around the first of January. Crowds have never been a problem for us. That being said, we visit the Magic Kingdom early in the morning and leave about 11:00 or 12:00 and park hop. As far as the Marathon, this year we arrived the day of the marathon and it was gridlock trying to get to our hotel. I would suggest avoiding arriving or leaving the day of the Marathon and it won't be too bad.
We have to WDW the past 2 years arriving on January 1st. 2005, crowded the first 2 days, then thinned out quite a bit. This year, it did not seem to thin out at all, guess each year is different. We are planning for January 1st, 2007, this is the best week for us to go. Make good use of EMH, fast pass, ADR's, and anything else possible to help deal with the crowds and you should have a great trip, we did.