Tiled is a cross-platform map editor application. It's got unlimited map layers and an isometric/hex tile mode, and has some interesting features for displaying large objects as single tiles (extra height displays above like with priority in RMXP but does not take up additional tiles...kind of hard to explain I guess). It's up to the developer to implement in-game map display based on the data format, afaik. The biggest problem with it is lack of autotiles, which has prevented me from looking into it more as a replacement for RMXP's map editor. But, if you're just drawing the maps and breaking them up into square tiles or using them as a panorama anyway, I think it would work just fine to take screenshots from inside the application.