I've toured on the Scwalbe Marathon, and the Continental Gatorskins. Probably 6,000 miles each of touring on my bike and my wife"s bike with the Marathon tires with a total of 6 flats. I have much more experience with the Gatorskins, don't know the number of flats/ miles ridden. The tour I do have numbers for was a 3700 mile cross country ride where we had a total of 13 flats with 28 mm Continentals. Several of those were in "goat head" country, and we rode through several large cities. We were also riding on pretty worn tires by the end of the trip. But we have ridden the Ultra Gatorskins a lot over the last 10 years, and after this summer's ride my wife won't let me put anything else on her touring rig.
Recently I switched from the Marathons back to 32 mm Gatorskins. On a receent 1200 mile ride I had 2 pinch flats, which were probably my fault for letting my front tire's pressure get too low. I like the feel of the Continentals over the Shwalbe tires, not to mention the weight difference. I would have gone to the 32 mm Gatorskins earlier, but the 32 mm tires were not available in the U.S. until recently.
This is purly my perception, but I think the Marathon tires are a little better for flat protection. However, i'm willing to change a few tubes once in awhile for the handling and weight saving I perceive getting with the Continentals.