Generally there are 3 engine placements:
In the tail, on the fuselage in the back, or under the wings. I'll go over the pros and cons of each.

On the tail: Not many pros, except that it lets one turn a four-holer into a three-holer which is usually more efficient. The cons are generally that- if you lose the engine in the tail, you risk losing rudder control and you also need a throughly reenforced tail, plus you have fuel lines running near the cabin, and you have a significant amount of weight not near the center of gravity.

On the fuselage in the back: Pros: Helps to prevent debris from entering the engine, allows for more room for flaps on the wing, and lighter, more aerodynamic wings since they are not holding up engines, generally allowing for slower approach speeds, also the thrust is closer to the center of the aircraft. Cons: Fuel lines near the back of the aircraft,tail has to be a T-tail, as well as reinforced. and center of gravity issues.

Under the wings: Pros: Well centered with the center of gravity, allows for more weight shifting in the cabin, and with the bags. The fuel is also kept away from the cabin, and the noise is better spread out through the cabin. In the event that something goes wrong, debris is also less likely to enter the cabin. Cons: Much easier to get debris swept into the engine, wings have to be reinforced, lose some area for flaps and slats, raising approach speed.

Some useful links:
http://adg.stanford.edu/aa241/propulsion/engineplacement.html
http://www.airliners.net/aviation-forums/general_aviation/read.main/750042/