I'm certainly no expert on drivelines but I do know one thing that's helped me to understand the most common source for driveline vibrations.
Here's the thing... If you were to put a degree wheel like you'd use for degreeing a cam on the output shaft of the tranny and another degree wheel on the driveshaft you would find they would only read the same at two places per revolution. The working angle of the U joint causes the driveshaft to go faster then slower than the transmission twice every revolution. The greater the working angle is the greater this effect will be.
So, if you've got a 5 degree angle at the front U joint you're probably going to feel a vibration unless you do something to correct it. All you have to do to correct it is use the same 5 degree angle at the rear U joint. That way the output shaft of the transmission and the pinion of the differential will be spinning at exactly the same speed through all 360 degrees of each rotation.
For a single driveshaft the pinion and the transmission output shaft should be parallel to each other but as others have said the suspension will wind up under acceleration so it's usually best to aim the pinion down a bit to compensate. How much lower you go depends on your suspension and how you use the car. For a drag car you probably want the driveline angles to be perfect under hard acceleration but for a cruiser you probably want the angles perfect at light load and let them be off a little under full load and braking. The angles won't be perfect under all conditions, and they don't have to be, as long as they're close you won't feel any vibration. My guess is that aiming the pinion down about 2 degrees less than parallel to the transmission output shaft would be about right for a street driven car with leaf springs and maybe as little as 1 degree for our X frame cars with the three link suspension. For a drag car you'd probably want to point the pinion down an extra degree or two.
When it comes to the two piece driveshafts like we have in our cars, I don't really know how to compensate for the angle at the center U joint. I don't know how hard it would be to figure out, but I don't know how it's done.
I don't have a manual here but if I remember correctly our cars don't use the regular parallel method of U joint angle cancellation. I think they use the less common "broken back" method. The second driveshaft in the picture below shows the broken back method, it looks weird but it works.