In some schools, so I understand, AP and Honors courses come with a "bonus" to GPA—so if you get 100% in the course, it may go down on your transcript as a 110%, that sort of thing.
My school had a pretty good system, where AP grades got a boost proportional to how far from 100 they were, something like 40%, so if you got an 80 raw it would be boosted by 20x.4 = 8 to 88 final score. This effectively means that weaker students aren't penalized for chosing harder classes whilst very strong students don't get rediculously inflated grades.