Body Paint 3D does this. You have to mess with the brush setings quite a bit to get decent paint, but you can paint to separate channels simultaneously. Deep Paint 3D also does it, but I hated their paint tools back when I messed with it.
Increasingly I work with multiple texture layers in photoshop..layers for diffuse, specular, normals etc. I would love to be able to use some tools on multiple layers at the same time. The most common use would be fixing seams on tiling textures using clone tools. Right now I end up fixing each layer seperately, which…