The entire design of the Object Manager (which extends itself to the tag and material management systems as well). Honestly, that is what separates C4D from other programs in terms of ease of use (IMHO) and what keeps me from going deeper with Blender and pushed me away from modo many years ago. Also, for very large scenes, I can have two object managers which is extremely helpful when you want to start organizing things a bit better.
Now, I have not compared C4D's OM to other programs (Maya and Houdini in particular) so if there are elements of scene/object management in those programs that are better than C4D's, please speak up as I would love to hear them.
Dave