High-end experts like turbocharging guru Ken Duttweiler and EFI University's Ben Strader have spent countless hours on the dyno and in the lab playing with fuel-injector location and angle. 
There are several observable trends from this research, but in the end, any individual engine may deviate from theory or previously observed trends, so the following should be taken as only a baseline recommendation, as your outcome may vary.  
Basically, there are three factors that have to be juggled: idle quality (which would also include emissions in an OEM smog-legal application), proper fuel/air atomization, and the physical constraints of the engine and intake-manifold configuration.  
These factors combine to determine injector location and angle within the intake manifold's inlet runner.  In a perfect world, nozzle location should be as parallel to the airflow stream as possible.  
The nozzle angle in relation to the airflow stream is termed the "intercept angle."  According to Strader, the intercept angle should "not be more than 45 degrees, although it can be less." 
Maintaining the proper intercept angle generally helps low-speed driveability and may also improve performance throughout the engine's operating band.  
The lower the inlet airspeed at idle, the more critical it is to maintain the ideal intercept angle.  Idle vacuum correlates well with inlet airspeed-if you have 14-18 inches Hg of vacuum at idle as read on a vacuum gauge, maintaining the proper intercept angle is not as much of an issue in terms of driveability, although there still could be some emissions ramifications. 

Fuel Injection Two Duttweiler sheetmetal intakes:
​A 1,600hp Buick V-6 high-rpm drag-race motor responded  So much for injector angle-what about injector placement?  
Should it be closer to the valve (downstream, near the cylinder head) or closer to the air meter (upstream, toward the top of the inlet runner)?  It depends on the engine and application. 
A stocker is primarily concerned with idle quality, low emissions, fuel mileage, and engine-compartment packaging constraints.  
On a stocker, fuel-injector capacity (rated in lb/hr) is low (compared with a race engine), while inlet-runner velocity and low-speed vacuum are high.  
The small-capacity nozzle develops a good spray pattern that disperses uniformly within the incoming air stream. With good atomization, the nozzle can be located downstream, close to the valve. 
Small injectors don't have a lot of fuel to waste, so targeting the spray toward the back side of the valve ensures that the available fuel is used most efficiently. 
 On the other hand, in theory, high-idle vacuum generated by mild stock engines permits placing the injector farther upstream without significant low-speed driveability degradation.  

In the end, OEM-style downstream injector placement simplifies system packaging and makes it easier to mount the fuel rails.  Everything changes with really large injectors (over 96 lb/hr).  
High-capacity injectors generate a relatively poor spray pattern with a large fuel-droplet size. As Duttweiler puts it: "You're practically just spraying raw liquid.  
If you put a big injector too close to the valve, there's not enough time for the fuel to mix with the air." Large injectors would most likely be used in large-displacement or high-rpm engines with lumpy cams.  High rpm translates into less time between injector firing pulses, lumpy cams generate poor vacuum, and the typically large-volume inlet runners needed to feed all those cubes generally mean lower air velocity downstairs.  
Obviously, all this adversely affects proper fuel atomization.
Moving the injector farther away from the valve allows more time for the air/fuel to atomize properly and remain in suspension when air velocity comes up at high rpm.  
This should improve peak power but-because of poor low-rpm velocity-at the expense of idle quality (there's no free lunch). 

Looking at some real-world examples, Strader reports that on a 1,000hp engine, the injectors were originally located 7 inches back from the valves.  
Doubling this distance to 14 inches was worth 50 hp on top, a 5 percent gain-but "it wouldn't idle below 1,600 rpm."  For an even more extreme example, consider the injector placement on today's 15,000-rpm Formula I engines.  
The injectors, wiring harness, and fuel-distribution rails are located topside, even inside the manifold plenum area, so they can maintain the proper intercept angle.  

In the real world, mass-produced aftermarket cast-aluminum manifolds have the bosses added as an afterthought to a preexisting design.  
The placement is more for convenience than for best engineering practice-the available packaging architecture (including fuel-rail mounting and clearance) to a large extent dictates the nozzle location.  
A decent compromise for a hot-rod engine is to locate the nozzle about 1-2 inches upstream from the manifold flange to give atomization a chance, positioning the fuel rail at the best angle you can get away with and still package the harness and fuel rails.  
As Duttweiler puts it: "If you aim the injector more toward the valve, the fuel rail usually hits the plenum" on a converted classic V-8 carburetor-style intake.  
Note that at the OEM level, the trend on today's new-tech V-8 engine designs is to make them wider than a similar-displacement, old-school, classic engine.  
The included valve angle in some of the new late-models is nearly straight up and down in relation to the bore.  That means the runners are also near vertical, which in turn allows mounting the injectors more vertically to provide room for the fuel rails and wiring harness while still maintaining a good intercept angle to the runner.  

​Duttweiler Performance Saticoy, CA 805/647-5732