For last couple of days I was working to have Tiled work as 3D map editor. I’m pretty much finished, the only thing left is to have particle system support, which shouldn’t be a hassle.
Right now I can create a map in Tiled, and based on two json files (one for tileset definition, second for entity definition)  I can create maps with multiple stacking levels, spawn points, triggers, 3D decorations, and configurable entities also with full physics. So not bad for a week of after hours work Now only some minor details left (like the particle effect and changing the scripting mechanism) and fixing my broken animation editor which has been non functional and waiting for some debugging love for the last 6 to 8 months.

Map in Tiled

 Visualization in game (yup debug textures and meshes :P)