I know that this issue has been around for a long time, but I would like to make a note of it in the official bug tracker.

Clouds still pass through solid objects in their path, instead of becoming transparent. I've heard that Mojang is reworking the rendering engine for Minecraft and it would be nice if they finally fixed this issue.

I've attached a gif I have seen around multiple sites, most likely coming from this: http://www.reddit.com/r/Minecraft/comments/e7xol/this_is_how_clouds_should_work_gif_simulation/

I don't know if that method would work, but it would be nice to get someone at Mojang talking or thinking about this issue again.