I expected to buy the '06 Prius, but after test driving I found the Civic handled much better and didn't have as much cabin noise. The only disappointment I've had is the fact the engine "auto-stop" feature (when stopped at a light) doesn't always kick- in. The manual explains some of the reasons this doesn't always happen, but there are still some times I can't figure why it doesn't shut down. That's minor, though, in light of the excellent "green rating" (#1 on some lists) and my overall satisfaction - I HIGHLY recommend this car!
Civic Hybrid comes with everything standard - Toyota makes you buy expensive packages to get any of their bells-and-whistles. Added bonus: Honda has the best built-in Navigation system out there - ask anyone who uses it.
Slight adaptations to trunk (height, depth) - it's difficult to fit 2 large suitcases.