It counts the same towards your GPA, but probably wouldn't be seen as being equal to their in-class counterparts. The fact that you did poorly in them might be worse than if you'd gotten the same grades attending a university. Online classes are notoriously easier than the others.
As far as retaking/taking new courses, if you did very poorly on your first time through of some of the basic sciences, you might consider retaking them just to understand the material better. They won't replace your original grades, but will be averaged with them (considered a new class).
If you're talking about as far as admissions committees go, it would probably make a better impression to do great in a new class you've had no experience with, rather than doing well in a class the second time around. If I were on the admissions committee (and I'm not at all), I would expect a 4.0 from all retaken science classes, or question their motivation.