I think what "Star Trek: Armada" (a space rts) does is have a few plains with nebula texture, ghosted. I think that you should do this, but have all of the plains always pointing to the camera. That way, the nebula will look 3d, not like a bunch of plains. I think you should use about 10-20 plains. If you just had one plain, it would look strange how it appeared the same no matter from what direction you're looking at it. Even with a few plains, it would still look odd. Having at least 10 plains will make it look like a volumetric, 3d nebula. And EdzUp's idea of changing the fog when you enter the nebula is good.
You could do clouds the same way. It would work well for cumulus clouds, but you should only use multiple plains when you are close or inside the cloud. Otherwise, having 20 plain objects for every single cloud in the scene would be slow. You should use just one or two plains for clouds in the distance. Make the plains rotate slightly. As for stratus clouds, just use a horizontal plain with a cloud texture. That's what most games use, and it only looks strange when you pass through it (because it's completely flat and has no thickness). You should make the horizontal plain drift slightly (move along x and z axes). I might post some code later illustrating these concepts.
