The more I work with Rube the more features I'd wish to see in future versions pops up in my mind Here's extremely short list so far:
Layers
You might have a bunch of bodies really close or they do different things. It'd be great to be able to sort them into categories/layers in a panel similar to "items" panel. The thing I miss the most is to hide whatever you aren't currently interested in, perhaps hidden stuff won't be included in your final json either. Much like layers in photoshop/3ds max/flash etc.
Yeah, I have that in the feature voting. I thought it would be a close second behind the custom properties, but surprisingly it is quite low. Maybe you are dealing with more complex scenes than others
I also think this feature is important but i've put all my vote into the spritesheet feature as we cannot start working with rube in the office until it supports spritesheets and custom properties.
Maybe others have other similar reasons, where they urgently need some feature and they can live without some features that would help, but are not really necessary to accomplish anything in particular.
If layers included the ability to group any objects (images, bodies, etc.) and contained that layer information in the resulting JSON output, I'd be able to use the editor to help define my rendering operations.