There are several different ways in which you can organize the objects in your scene, depending on what you need to do:
Groups let you apply properties to all their members. The group property overrides members' local properties. Groups are also convenient for selecting objects, for example, you can add all deformers in a rig to a group for easy picking when enveloping. An object can belong to as many different groups as you want. See Grouping Objects.
Scene layers are similar to groups, but each object must belong to exactly one layer. You can apply properties to layers just like groups, but layers are usually used to control visibility, selectability, and renderability. For example, you could create one scene layer for meshes, another for bones and other deformers, and yet another for rig controls, and then display and hide them quickly using the scene layer manager. See Scene Layers.
Partitions let you override properties on specific objects when rendering a particular pass. For example, if you want to render certain objects constant black, you can create a custom pass, add those objects to a new partition, and apply a constant black shader to the partition. Like scene layers, each object must belong to exactly one partition per pass. See Passes & Partitions [Rendering].
Hierarchies are series of parent-child relationships between objects, forming a tree-like structure. You can see these relationships as nested nodes in the explorer and as links in the schematic view. Transformations are propagated down hierarchies, with each parent's local transformations being offset from its parent's center. You can also use hierarchies to propagate other properties, but locally-applied properties take precedence over inherited ones. See Hierarchies.
Transform groups are a specific case of a hierarchy with a null root to control animated transforms. See Transform Groups (Parenting with Null Objects) [Animation].
Models are a hierarchies that can be thought of as "mini-scenes". They have their own namespace, so two models can both have objects called "left_arm". They also have their own animation mixers, so you can control "left_arm" differently in each model. They can also be saved externally and reused by reference in multiple scenes. See Models [Data Management].
For a detailed description of how properties are propagated in groups, layers, partitions, and hierarchies, see How Properties Are Propagated.
