yEd supports the concept of grouping. Each group is represented by a group node that may be collapsed or expanded as needed.
Group nodes are available in the (lo and behold) "Group Nodes" palette section.
A set of selected nodes may be grouped using either "Grouping" -> "Group" or CTRL+ALT+G.
New nodes may be dragged from the palette into existing, expanded group nodes.
Existing nodes may be moved into existing, expanded group nodes by pressing and holding SHIFT while moving the node into the group.