Well, I've been using Unity3D engine for quite some time on the graphical side of things, I've always used it to create my maps and get everything set-up all nice and neat how I wanted it, I've also played around in UDK which is basically the same thing, but with more buttons.
However, the friend that I'm working with for our games has gone off to university and he no longer wants to use Unity3D, but the problem is, I'm the graphics designer for everything that we do, we share in writing the stories and he does the programming aspect.
He's recently moved on to writing games in java using OpenGL, however I have no idea how to help him with creating maps anymore, we've taken up Tiled for 2D map editing, which offers Isometric and Orthogonic Tile maps, but we've found nothing for 3D.
Incase some of you don't know what Unity3D was like when it came to world design, it was like this..
You could import models, and place them wherever you wanted them, scale them wherever you wanted them, texture it however you wanted to.
Basically it was a modeling program that allowed you to combine multiple models