I have only done Marathon Weekend so far, but here are my feelings on the subject:
Minnie 10k - Great course overall. A little boring to start navigating the parking lot and roadways around to the back of Epcot. From that point on, it was fantastic running through the World Showcase all lit up with the fires and Illuminations lights on the buildings. The loop around the Epcot resort lake was nice, too, although the wooden boardwalk was a little slippery due to rain early in the race. Probably my 2nd favorite course of the weekend.
Donald 1/2 Marathon - First, the highlight: Running down Main Street USA towards the castle and then through the castle a few minutes later were awesome! A highlight in my running career I'll never forget. Made me tear up. The lowlight: Just about everything else about the course. ~5 miles of parking lots and empty road to get to the MK. Then 6-7 miles of more empty road to get back to a brief stint in Epcot at the very end. I'm conflicted on this course because it was the highest high and the lowest lows. I'd have to rate it my least favorite course of the three overall.
Mickey Marathon - I know this is going to sound strange after the Donald review because the first third of the course is pretty much the same. Boring start, massive high running to and through the castle in the MK and then a long slog on the road to the AK. That being said, I really enjoyed the rest of the course through AK, WWoS (a little too much time there) and on through DHS. The finish was fantastic running past the Swan&Dolphin and YBC into Epcot with a lap through the World Showcase and past the ball to the finish line. Incorporating all 4 parks into the course made all the difference to me. My favorite course by far. I call the marathon medal my Ultimate Park Hopper!
I'm sure the fact that the marathon was my first is also playing into my feelings, but there you are. I'm running SWDS in a couple of weeks and the DDD in DL this summer so I'll have a better overall view of the different courses at that point if you're still looking for updates at that point. I don't think you can really go wrong with any of them, though.