I have run both.
I ran the January 1/2 in 2011 as part of Goofy (DH ran it in 2007 stand alone). I ran PHM this year.
I love the course but for the same reasons that Coach and the PP stated I hate the course. It has gotten too crowded.
Pros to Jan:
1. Corral placement seems to be better so there is less crowding, especially if you can get into A-C. This is a big factor in the fast men not being banished to C department (more on that later)
2. Weather on average is better in January (2013 was an exception, as was 2007 - we sure know how to pick lousy years to run!)
3. The overall atmosphere of Disney is more geared toward runners and running. You feel special and like the park is open just for Marathon Weekend because there is really nothing else going on.
4. The expo is better
5. Lots of characters on the course - I felt the variety was great and the lines are so short! maybe 1-2 people tops
6. If you are sub 2-hour you run in the dark so if it is hot you can beat most of the heat
Cons to Jan:
1. It is crowded
2. It is not the "crown jewel" of the weekend
3. You have to get there Friday to get your packet so you have to miss a day of work
4. Unisex shirts - they suck
Pros to PHM:
1. If you are into costumes and tutus, this is your race! The number not in costume is the vast minority, and we all look fabulous!
2. This is a chance to be placed high in a corral, 2:15 is in A, 2:30 makes it to B. That is fun

3. Gender specific shirts

4. The sun comes up so much sooner (You actually get to see the sun even if sub-2 hour)
5. This is the top race of the weekend
6. Sunday race so you can do packet pickup on Saturday
Cons to PHM:
1. Weather in Feb is less predictable - heat is much more common, but it can also be mind-numbingly cold. Likelyhood of rain is higher also.
2. Guys starting in C. This is not a good thing if you are starting in front of them and they have decided to try to "win". We were almost bowled over by guys before mile 1 (which is on a one-lane overpass). It is dark, we don't have our stride yet and all of a sudden you have people shoving you from behind. Rude and unsafe. I think the whole guys can't win thing needs to be rethought, it is dumb and makes for dangerous conditions on the course that is already overcrowded. I get the whole "girl power" crap, but it is out of control and something needs to be done.
Ok, off soapbox
3. Sun comes up sooner. I know I said that was nice, but on a hot day - man that can start to broil you quick! Just a thought!
4. There were not as many Princesses out for this race as I expected there to be so I was not impressed with that. Big Con for me! Plus when there was a character the line was 15-20 people deep!
5. Not as much of a race weekend feel
6. Not a great Expo
I love Disney and I love Disney races but I am frustrated with the sheer number of people on the courses. It is too many! There are several places where you are running on one lane of a road and you are really packed in. This is the same for both races since they have the capacity the same for both now so that is a wash. PHM might be less well-attended next year as it isn't an anniversary year but Jan will be popular with the new 10K and Dopey being added and then in 2015 it will be the 10th anniversary of Goofy so I see it being very popular for that year too. Let's face it they are super popular races every year! I don't think it will happen but I would like to see either a lower in race capacity to 15,000-18,000 or change the course to eliminate the cut-downs to one lane.