When the USAF and Boeing were discussing the 'plane that eventually became the XB-47, one of the requirements was to mitigate the effect of an engine fire on the airframe. Boeing's answer was unusual. Mount the engine externally on the aircraft, not internally as had been the norm to that point, and so the under-wing, pylon mounted engine installation was born.
Today jet engines are still frequently mounted below the wing as it is a structurally convenient location to do so. In addition to all the info in the above messages, the spar and skin of the wings are already "beefy" to take the shears and bending moments of flight, so not much additional thickening is required to react the loads of a wing-mounted engine. Aft fuselages without an aft-mounted engine tend to be fairly light, but placing engines in this area introduces significant additional structure (and thus weight) in order to take the loads. This is offset, to some extent, by the opportunity of using a shorter, lighter landing gear as in this case there is no protuberance beneath the wing to worry about.
This is made less straight-forward by rotation angles and runway clearances. When taking-off with a long fuselage, it is easier to get a tail strike on rotation, so to counteract that, longer 'planes tend to have longer gear. So if you have a long aircraft, you may as well use a wing-mounted, under-slung engine as you are stuck with using a tall, heavy landing gear anyway, and the wing is a good place to mount the engine. If you have a short aircraft and you can get away with a shorter, lighter landing gear and still achieve adequate runway clearance on rotation, then go for an aft-mounted engine and retain the short, light gear. Just beware of adding too much additional structure in the aft fuse to carry the engine.
There are many exceptions. The originally short DC-9 with aft-mounted engines was eventually stretched into the long MD-90 (although they tried hard to do most of the stretching forward of the landing gear to reduce the tail strike issue, I think), and the A320 with its under-slung engines and long gear was shrunk to the short A318. However, that these derivatives both are a long-way removed from their original concepts and they inherited their configurations. And there is also the case of high-wing aircraft, like the C-141, but they have to have different requirements compared the usual Airbuses & Boeings.
I recall that Dan Raymer's "Aircraft Conceptual Design" has a nice summary of engine-mounting options.
FastMouse