Out of the three examples, Wired for the ipad has some of the most attractive examples of the new tablet magazine format and the consequent inovations. They've really taken the user experience into consideration. The user can take part in an enveloping experience which can take place in many individual elements, and can go on for several layers of interaction. This is not only a breakthrough for the magazine articles and overall story, but also for the advertisements. My favorite example of this is the ad where the interface allows for a 360 look around of a car.
The Esquire magazine's ipad format is as equally layered and intuitive, but I find the Wired layouts more attractive as is usual. They seem to have more first level interaction, but allot of it. It also has the option to scroll through pages with a table of contents that lets you see thumbnails of the full pages. The Wired version also gives you the option to simply scroll without the thumbnails. It seems to me as though the layouts share a closer aesthetic to a standard handheld paper magazine.
The time magazine has something that somewhat stands out from the others, in that it has assigned different functions to the vertical and horizontal format of the ipad. It also has a standard magazine feel to it with the exception of some video and picture interaction. When put in a horizontal position the layouts often become more visual than text based.