I own both. An 06 Prius Pkg. 6 and an 07 HCH w/ Navi. My wife drives the Prius and I drive the HCH. The decision for me was pretty easy. It came down to one thing, styling. I like the looks of the 07 HCH better. My wife likes the looks of the Prius better.
As hybrids go, it's my opinion that the Prius leans more towrds "electric" then the HCH. I believe it's technologically more advanced then the HCH. The mileage is pretty much neck and neck between our 2 cars with a slight edge to the Prius. I would also give a slight edge to the Prius for acceleration. The HCH handles better but lacks tire pressure sensors and rear view camera. The Prius has more cup holders and storage compartments then I would know what to do with.
We both have HOV Stickers and use our hybrids as commuter cars. I'd rather drive my HCH and my wife would rather drive her Prius.
Having said all that, I guess her vote cancels out my vote.