I did the marathon this year for the first time, and I would say it varies, with characters most prevelant around the parks. First was Chip and Dale at mile 3 in Epcot, missed Tinkerbell at about mile 6, and then got Tigger and Eeyore at about mile 7-8. Then in MK got StepMother/StepSisters and passed on Fairy Godmother. Also got Princess and Frog crew (Tiana, Prince ?, and Louis), Woody/Jesse, and POTC crew (my vote for best costumes). So the MK stuff was all between mile 10-11. Then about mile 12 got Goofy/Donald on a golf course. Somewhere around mile 14 got PP/Wendy/Hook/Smee. Then at AK got Belu/King Louie, then Minnie, and then Mickey. Then at DHS (mile 21-22 ish) got Russell from UP, and then Phineas/Ferb. Back in Epcot got Jasmine, then Snow White, and then Mulan/Mushu.
So that was 16 different character opportunities that I did. Besides missing Tink and Fairy Godmother, I probably also passed on 3-5 others...can't come up with them at the moment.
They are plentiful, and was one of the reasons I decided to do Disney. Sure, it probably tacked on 15-20 minutes to my run, but each time I thought..."in 5 years would I rather have a picture commemorating this event, or a couple more minutes of time." Picture won out most of the time!