At my school, weighted GPA is on the scale: AP: 6.0, Honors: 5.0, Regular: 4.0. We also have an "Academic Core" GPA which is: AP: 5.0, Honors: 4.5, Regular: 4.0. Which, if any, do colleges use?
Colleges will almost certainly focus more on your Academic Core GPA out of 5.0 than your overall GPA out of 6.0. Admissions officers are primarily interested in your performance in core subject areas. Your overall weighted GPA may not reflect your abilities as accurately if it's inflated from electives or less challenging classes outside of the core requirements.
Keep in mind, however, that colleges will still see both GPAs, so they don't exclusively "use" one or the other. It's just a matter of which one carries more weight in the admissions process.