The first thing we'll discus is ruins. Most people play them as area terrain and are under the impression that should you be in them, you receive a 4+ cover save. This is not correct. As they are area terrain, you receive a 5+ cover save and only get the 4+ if the model is physically blocked by part of the ruins.
As long as we're discussing area terrain, here is another tidbit- going to ground will normally grant you a +1 bonus to your cover save, but going to ground in area terrain confers a +2 bonus! This coincidentally means that if you're in ruins that are area terrain, go to ground, and are 25% obscured you get a 2+ save! Some people may argue with this that the +2 only applies to the save granted by the area terrain, but the benefit from going to ground in area terrain applies to all the models cover, not just that granted by the area terrain.
An important change to note with 6th edition is also that area terrain has no effect on models shooting out of it, unless their target is actually obscured.
Hopefully this will make your future dealings with cover saves more understandable!