I think it totally depends on the rest of your application. I had a 3.71 total GPA. My science GPA was about a 3.5, my AO GPA was a 4.0. I am now a fouth year at my first choice medical school. For me, my AO GPA was a benefit to me, even though I took some knocks in my science classes. I took some difficult non science classes like Modern American Literature because I thought they were interesting. Also, explaining why you recieved a B in Organic is much easier than explaining why you had a low grade in a non-science class.
That being said, great science grades at the expense of some non-science classes sometimes happens as well. It is hard to study for those history finals, when you are spending hours in the lab getting an A in Organic Lab!
All in all, just be prepared to explain anything to the adcom.
Good Luck. 😉
And please, for the anal ones reading this, do not attempt to reconcile the math in my GPA. I no longer remember how many hours of what I took during my bio major liberal arts days, luckily I remember very little from what I learned/did in undergrad,except for the previously mentioned American Lit.