I would say many sites have been stripped of their ability to pass PR and this has a knock on down the line > some of your back links now count for less or nothing at all I suspect this is especially true of web directories, even if the directory still has TBPR I very much doubt the links pass any PR at all. I also notice many directories now have PR0 on inside pages. So I think if you want higher PR it will not come from directory submission in the future
sites dropped not because of a penalty of the type links pointing to them. they dropped because the links are flowing less pr. if you are pr 5 and now pr 3 its just the in bound links have less pr from the our going sites. the big directories had pre-arranged network links that google considers paid so they loose juice. So the directories go down and as links are re-assed then sites will bounce up and down. I guess in a week it will settle - i dont see youtube as a 3 for long..