The literature on "3D Bin packing" is far and wide. You can get a good overview by tracking the publications of Professor David Pisinger. He also published one of the few high quality implementations of bin packing with sourcecode: 3dbpp.c
My own logistics toolkit pyShipping comes with a 3D Bin Packing implementation for Warehousing applications. It is basically implementing 4D Bin Packing (3D size & weigth) and gets an acceptable solution for typical order sizes (a few dozens of packages) in under a second runtime. It is used in production (meaning a warehouse) for some months now to determine the upper bound of shipping crates to be used. The warehouse workers are often able to pack somewhat more efficiently but that's OK with me.
