I see more and more wireframes looking like this :
I need to explain an imbricated and layered structure to someone, so I want to use images like that.
Is there a tool that already does that, or do I still have to do it myself using Photoshop ?
I'm not aware of an app specific to this task but there are a number of Photoshop actions that may help achieve the look you're going for. This page has a couple that may suit: http://designbeep.com/2013/10/04/15-free-perspective-screen-mockups-showcase-app-design/
Actions with potential: Basic Mobile App Screen Mockup, Isometric Perspective MockUp, Screen Layers
And if these don't work you can always record your steps while adjusting your layers and perspective and use them again later for other tasks.
So far I haven't found any app doing this.
I have been using Photoshop to do it. With Photoshop CC 2014.2:
file > place linked.
3D > new postcard from layeror
3D > new mesh from layer > postcard