How does the mounting location of a jet engine affect aircraft performance?
Engine location performance-affecting factors:

1. Mounted in the wing root


low asymetric yaw on engine failure, less rudder required: less drag
no engine pods: less parasitic drag
engines closer to CG, less downforce needed from the tail:  less drag
very little reverse thrust available
Little space for high-bypass-ratio engines


2. Mounted in pods under the wing


high asymetric yaw on engine failure requires larger rudder: drag penalties
engines provide bending relief on the wing, allowing better wing design (thinner wings): less drag
at high incidence angles the pods can prevent spanwise flow: less drag and better stall characteristics 
full thrust can impose a large, undesirable, pitch up moment (think stall recovery)
less freedom in roll on cross-wind landings
Location ahead of the wing's elastic line helps to dampen flutter


3. Mounted inside the tail or on pods on the rear fuselage


low asymetric yaw on engine failure, less rudder required: less drag
wing design is freed from the need to accomodate engines, allows for more complex wing designs: better performance throughout the flight envelope
heavy engines so far aft of the fuselage require wings mounted further aft, and a higher tail to support that: more drag
Lower landing gear required, especially in case of short fuselages


That's about what I can come up from memory, maybe someone can merge all answers into a comunity wiki kinda post..