I haven't stayed at the Polynesian since I was little and don't remember much of our stay there, but we did just recently get back from the Contemporary Resort.
Having said that, I'll also cast my vote for the Polynesian. We don't necessarily have any complaints about the Contemporary, but there's a definite lack of theming. Other than the fantastic location and the monorail, it felt like a hotel in any other city to me.
We did visit the Polynesian for a few meals, however, and it just has much more of a "vacation" feel to us. All the lush plants, the waterfalls and tiki torches make you truly feel as if you're someplace tropical and exotic. If we had stayed there, we would have definitely taken more time away from the parks to simply enjoy the resort and relax. At the Contemporary, we didn't feel like we wanted to spend any time there other than to sleep.
Although we'll stay at SOG on our next trip, we definitely have the Polynesian on our radar for the future. As far as the Contemporary goes, we're glad we got a chance to check it out, but we're in no rush to go back...