Advantages and disadvantages of air intakes above fuselage/wings in jet fighters?
Advantages of overwing intakes:


Little danger of foreign object damage (FOD). Remember that F-16 bases need to keep their runways spotless in order to avoid FOD. The low intake will hoover up all loose items around it while the overwing intake mainly sucks in air from above.


Disadvatages of overwing intakes:


Lower pressure recovery at high speeds. The air above the wing is first accelerated in order to create lift and then this accelerated air must be decelerated for maximum pressure recovery. This is less direct and incurs more losses than low intakes which operate in pre-compressed air.
Operation in low density air in supersonic flight. Especially when thrust is needed most, at high angle of attack, an overwing intake will feed the engine with lower pressure and lower density air, reducing the available thrust.
Noise: The North American F-107 was said to be the loudest aircraft from the pilot's perspective, and cockpit noise was one reason why it did not enter production. Granted, here the intake was not over the wings but on the upper side of the fuselage, right aft of the cockpit, but I thought I include this item here nonetheless.



Early stage of F-107 development (picture source), at this time called the F-100 B, but the low intake interfered with weapons release from a central belly bay …


… and that is how it turned out eventually with the re-located intake (picture source)