Since nobody has so far, I will put in my own personal plug for the HCH. It's a great car- I absolutely love mine. I have the HCH I, not the newer HCH II (which is what the 2007 model is) so my comparison shopping, which came down to the same decision you face, is a little bit old, but I think that many of the same principles still apply.

1) the Prius is more expensive. This is a deal breaker for many people. But there isn't a wait anymore, and the pricing is apparently getting more competitive, so if you decide you want the Prius, you can try negotiating and see how you do.
2) the Civic is a little bit smaller. I did not care about this, particularly. You might.
3) the Prius is rated at significantly better fuel efficiency. You can check our database for more accurate numbers, which reflect real-life results from actual car owners. Currently the Prius II averages 48 and the Civic II averages 46. These numbers have changed a bit over time- but the difference has never been close to the EPA ratings difference. It's a couple mpg- and individual results vary far above and below the averages. You can do as well or better in an HCH than a Prius, but that's going to depend on you and your driving conditions, etc.
4) You mention a difference in the EV mode. I understand that the HCH II has some new features in terms of moving while on the electric motor that my car doesn't have, but I will leave all comments on that subject to someone who knows more about it than me.
5) Then there's the 'image' factor. Some people like the fact that the Prius looks a little alien and stands out in a crowd. Some people like the fact that the HCH looks like a non-hybcar and blends in with 'regular' cars.
6) For me, one of the big deciding factors was the rear spoiler in the middle of the Prius's windshield. I felt like it was a safety issue for me, because I couldn't see out the back very well. This is apparently not a problem in the Prius II design. But it's little wacky stuff like that which is really noticeable during a test drive but you'd possibly never know about just by doing research- and only you can say how much some quirk like that bothers you.

Good luck! It's a hard decision, but really you can't go wrong, because they're both fantastic cars. Welcome to Green Hybrid and I hope you enjoy whatever car you decide to buy.