How is it possible to make Eagle parts containing multiple components?
What you're describing can be done in the Eagle library manager.  Essentially, Eagle will treat your aggregate component as an integrated circuit.  You can create a PCB footprint in Eagle, with multiple pads.  For example, pads 1 &amp; 2 are the LED, 3 &amp; 4 are resistor.  Eagle allows to draw wires in the component editor.  When you route the rest of your board, these wires will be fixed to the footprint and will not be routable.

If you are going to assemble your board with a pick &amp; place, you will need coordinates for the components.  Eagle will produce only one (1) set of coordinates for your aggregate part, even though it has several separate parts.  You would need to find a way around this.  But, if you'll be assembling the boards manually, you will not have this problem.

Other design packages (OrCAD, Altium) support hierarchical blocks.  At a minimum, hierarchical blocks let you reuse schematic.  Some EDA software supports hierarchical blocks with PCB layout reuse.